Bgee: Gene Expression Evolution

Expression data retrieved for the gene ENSG00000175518: UBQLNL - Homo sapiens

Query parameters
Gene: ENSG00000175518 - UBQLNL
Data parameters
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Hide | TopRNA-Seq

RNA-Seq experiment GSE30352

Experiment name The evolution of gene expression levels in mammalian organs [GSE30352]
Source GEO
Experiment description Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes.
Samples
  • Sample ID: GSM752707 - log2 RPK threshold: -4.615 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000121
    • Gene ID: ENSG00000175518 - log2 RPK score: 1.944 - Detection flag: present - Quality: high quality
  • Sample ID: GSM752708 - log2 RPK threshold: -1.469 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000095
    • Gene ID: ENSG00000175518 - log2 RPK score: 4.515 - Detection flag: present - Quality: high quality

Hide | TopAffymetrix

Affymetrix experiment E-AFMX-11

Experiment name Transcription profiling of humans and chimpanzees in brain, heart, liver, kidney, and testis [E-AFMX-11]
Source ArrayExpress
Experiment description The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.
Chips
  • Chip ID: ht4 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000121
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: ht2 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000118
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: ht1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000128
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: ht5 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000123
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: ht6 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000115
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: ht3 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000115
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-2030

Experiment name Transcription profiling of human blood taken from individuals fed an antioxidant-rich diet or a diet containing kiwi-fruit to evaluate the effect on gene expression with emphasis on stress and repair related processes [E-MEXP-2030]
Source ArrayExpress
Experiment description Plant-based diets rich in fruit and vegetables can prevent development of several chronic age-related diseases such as cancer and cardiovascular diseases. The mechanisms behind this protective effect is not elucidated. We have studied whether a specially designed antioxidant-rich food diet and a kiwi-fruit intervention can affect whole genome expression in human blood cells with emphasis on stress and repair related process.
Chips
  • Chip ID: OAS59-1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000139
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: OAS13-1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000155
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: OAS61-1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000155
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: OAS92-1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000146
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: OAS12-1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000148
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality

Affymetrix experiment E-MTAB-54

Experiment name Transcription profiling of gluteal and abdominal fat biopsies and whole blood from obese and normal weight patients [E-MTAB-54]
Source ArrayExpress
Experiment description Experiment on MolOBB dataset by Novo Nordisk. Expression profiling of gluteal and abdominal fat biopsies and whole blood from obese and normal weight patients.
Chips
  • Chip ID: MolOBB_Plate3_B7 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000148
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: MolOBB_Plate_3_A1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000140
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: MolOBB_Plate2_F7 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000139
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: MolOBB_Plate2_G11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000139
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: MolOBB_Plate_3_C9 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000148
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality

Affymetrix experiment E-TABM-940

Experiment name Transcription profiling of human blood from patients with ALS vs healthy [E-TABM-940]
Source ArrayExpress
Experiment description ALS whole blood samples or non diseased control whole blood samples hybridized to HgU133vII Affymetrix genechips. As a factor value for experiment clinical history has been used including: 1) the ALS FRS score that provides a physician-generated estimate of the patient's degree of functional impairment, which can be evaluated serially to objectively assess any response to treatment or progression of disease. The ALS FRS score includes ten questions that ask the physician to rate his/her impression of the patients level of functional impairment in performing one of ten common tasks, e.g. climbing stairs. Each task is rated on a five-point scale from 0 = can't do, to 4 = normal ability. Individual item scores are summed to produce a reported score of between 0=worst and 40=best. And 2) Forced Vital capacity that is the maximum amount of air a person can expel from the lungs after a maximum inspiration. It is equal to the inspiratory reserve volume plus the tidal volume plus the expiratory reserve volume. The measurement is performed during forceful exhalation. It reports the largest value of three technically satisfactory maneuvers. The three FVC measures should not differ by more than 150 mL from the next largest FVC, or 100 mL if the FVC is 1.0 L. If the difference is larger up to 8 measures should be performed.The percentage value is that compared to normal individuals of the same age and gender. 3) Date onset
Chips
  • Chip ID: 152394hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151987hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000155
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 152391hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000159
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 146139hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153573hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000148
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153175hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: absent - Quality: high quality
  • Chip ID: 151990hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151991hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000159
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 152390hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151992hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153574hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153176hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000160
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 152392hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151993hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153181hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 152393hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153178hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000142
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151988hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151989hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 151994hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153578hp133a21 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000140
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153575hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000139
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153577hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000142
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153576hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000154
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153174hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000152
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality
  • Chip ID: 153586hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000146
    • Probeset ID: 236965_at - Mapped to gene: ENSG00000175518 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE10780

Experiment name Transcription profiling of human histologically normal breast tissues reveals proliferative genes dominate malignancy-risk gene signature [GSE10780]
Source GEO
Experiment description Analysis of 143 completely histologically-normal breast tissues resulted in the identification of a malignancy risk gene signature that may serve as a marker of subsequent risk of breast cancer development. Experiment Overall Design: RNA was extracted from microdissected frozen breast tissues for gene array analysis
Chips

Affymetrix experiment GSE10810

Experiment name Transcription profiling of human breast cancer samples to distinguish phenotypes, histological subtypes and tumor invasivness [GSE10810]
Source GEO
Experiment description Background. The development of reliable gene expression profiling technology is having an increasing impact on our understanding of breast cancer biology. Methods. In this study, microarray analysis was performed in order to establish gene signatures for different breast cancer phenotypes, determine differentially expressed gene sequences at different stages of the disease, and identify sequences with biological significance for tumor progression. Samples were taken from patients before their treatment. After microarray analysis, the expression level of 153 selected genes was studied by qPCR. Results. A number of gene sequences were differentially expressed in tumor versus control samples and were also associated with different breast cancer phenotypes, ER status, tumor histology, and grade of tumor differentiation. In N0 tumors were found a set of genes related to tumor differentiation grade. Conclusion. A number of differentially expressed gene sequences were found at different stages of the breast cancer disease. Key Words: Breast cancer, gene expression signature, tumor invasiveness, microarrays, qPCR Experiment Overall Design: In total, 58 samples were studied, 31 tumors and 27 controls. Some of the samples are paired
Chips

Affymetrix experiment GSE10971

Experiment name Transcription profiling of human non-malignant fallopian tube epithelium and high grade serous carcinoma. [GSE10971]
Source GEO
Experiment description The purpose of this study was to identify molecular alterations potentially involved in predisposition to adnexal serous carcinoma (SerCa) in the non-malignant fallopian tube epithelium (FTE) of BRCA1/2-mutation carriers, given recent evidence implicating the distal FTE as a common source for SerCa. Experiment Overall Design: We obtained and compared gene expression profiles of laser capture microdissected non-malignant distal FTE from 12 known BRCA1/2-mutation carriers (FTEb) and 12 control women (FTEn) during the luteal and follicular phase, as well as 13 high grade tubal and ovarian SerCa.
Chips

Affymetrix experiment GSE11375

Experiment name Trancsription profiling of human severe blunt trauma patients to predict outcome [GSE11375]
Source GEO
Experiment description Physiological, anatomical, and clinical laboratory analytic scoring systems (APACHE, Injury Severity Score (ISS)) have been utilized, with limited success, to predict outcome following injury. We hypothesized that a peripheral blood leukocyte gene expression score could predict outcome, including multiple organ failure, following severe blunt trauma. Contributor: The Inflammation and the Host Response to Injury Large Scale Collaborative Research Program Experiment Overall Design: cRNA derived from whole blood leukocytes obtained within 12 hours of hospital admission provided gene expression data for the entire genome that were used to create a gene expression score for each patient. Expression profiles from healthy volunteers were averaged to create a reference gene expression profile which was used to compute a difference from reference (DFR) score for each patient. This score described the overall genomic response of patients within the first 12 hours following severe blunt trauma. Regression models were used to compare the association of the DFR, APACHE and ISS scores with outcome.
Chips

Affymetrix experiment GSE11622

Experiment name Transcription profiling of human post menopausal vaginal response and ovarectomised rat treated with estrogens [GSE11622]
Source GEO
Experiment description Background. Vaginal atrophy (VA) is the thinning of the vaginal epithelial lining, typically the result of lowered estrogen levels during menopause. Some of the consequences of VA include increased susceptibility to bacterial infection, pain during sexual intercourse, and vaginal burning or itching. Although estrogen treatment is highly effective, alternative therapies are also desired for women who are not candidates for hormone replacement therapy (HRT). The ovariectomized (OVX) rat is widely accepted as an appropriate animal model for many estrogen-dependent responses in humans; however, since reproductive biology can vary significantly between mammalian systems, this study examined how well the OVX rat recapitulates human biology at the transcriptional level. This report describes an analysis of expression profiling data, comparing the responses of rat and human vaginae to estrogen treatment. Results. The level of differential expression between pre- vs. post- estrogen treatment was calculated for each of the human and OVX rat datasets. Probe sets corresponding to orthologous rat and human genes were mapped to each other using NCBI Homologene. A positive correlation was observed between the rat and human responses to estrogen. Genes belonging to several biological pathways and GO categories were similarly differentially expressed in rat and human. A large number of the coordinately regulated biological processes are already known to be involved in human VA, such as inflammation, epithelial development, and EGF pathway activation. Conclusions. At the transcriptional level, there is evidence of significant overlap of the effects of estrogen treatment between the OVX rat and human VA samples. Experiment Overall Design: We analyzed vaginal biopsies from 19 woman pre and post 3 month estradiol treatment and compared to OVX rats treated with E2 for 6 hr, 3 days or 5 days (N=5)
Chips

Affymetrix experiment GSE11952

Experiment name Transcription profiling of human small airway epithelium responsive to smoking reveas coordinate control of Nrf2 mediated genes [GSE11952]
Source GEO
Experiment description Nuclear factor erythroid 2-related factor 2 (NFE2L2, Nrf2) is an oxidant responsive transcription factor known to induce phase 2 detoxifying and antioxidant genes to protect cells from oxidative stress. Cigarette smoke, with its large oxidant content, is a major stressor to the small airway epithelium, the cells of which are vulnerable to oxidant damage and consequent malignant transformation. In this study, we assessed the role of cigarette smoke in activation of Nrf2 in the human small airway epithelium in vivo. Fiberoptic bronchoscopy was used to sample a pure population of small airway epithelium in 38 healthy nonsmokers and 45 healthy smokers, and gene expression was assessed using Affymetrix HG-U133 Plus 2.0 microarrays. Compared to that of healthy nonsmokers, Nrf2 protein was significantly activated in the small airway epithelium of healthy normal smokers and localized in the nucleus (p<0.05). Of the human homologs of 201 known murine Nrf2-mediated genes, 13 highly smoking-responsive genes were identified (p<10-4, all comparisons smokers to nonsmokers). Using a Nrf2-index to quantify the extent of expression in the small airway epithelium of these 13 known Nrf2 genes, variability in the level of expression was observed among the 45 healthy smokers, but the variability was coordinately modulated among the 13 genes, an observation confirmed by TaqMan quantitative PCR. This variability in the coordinate level of expression of the 13 Nrf2-mediated genes was independent of the smoking history. Based on these observations, the Nrf2 index was used to evaluate whether other genes modulated by smoking in the small airway epithelium were also coordinately up- or down- modulated among the 45 healthy smokers. Two genes, pirin (PIR) and UDP glucuronosyltransferase 1 family polypeptide A4 (UGT1A4), not previously known to be modulated by Nrf2 were identified as being coordinately modulated among the 45 smokers. Both genes contain several functional antioxidant response elements in the promoter region. Using an electrophoretic mobility shift assay, these antioxidant response elements in the promoters of PIR and UGT1A4 responded in vitro to activated Nrf2. These observations are consistent with the concept that Nrf2 plays an important role in regulating cellular defenses against smoking in the highly vulnerable small airway epithelium cell population, and that there is variability among the population in the relative Nrf2 responsiveness to a similar oxidant burden. Experiment Overall Design: Affymetrix arrays were used to assess gene expression data in small airway epithelium obtained by fiberoptic bronchoscopy of 38 healthy non-smokers and 45 healthy smokers
Chips

Affymetrix experiment GSE13355

Experiment name Transcription profiling of human skin from psoriatic patients and normal controls [GSE13355]
Source GEO
Experiment description Gene expression has been proposed as an intermediate phenotype that can increase power in complex trait gene-mapping studies. Psoriasis, an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints, provides an ideal model system to evaluate this paradigm, as conclusive evidence demonstrates that psoriasis has a genetic basis and the disease tissue is readily accessible. To better understand the complex nature of processes in psoriasis, we characterize gene expression profiles in uninvolved and involved skin from affected individuals as well as normal skin from control individuals. Experiment Overall Design: We extracted total RNA from punch biopsies taken from 58 psoriatic patients and 64 normal healthy controls. Two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample), taken at least 10 cm away from any active plaque. One biopsy was obtained from each healty control. Totally 180 samples were run on Affymetrix HU133 Plus 2.0 microarrays containing >54,000 gene probes. Experiment Overall Design: The raw data from 180 microarrays were processed using the Robust Multichip Average (RMA) method. The expression values in the table were after adjustment of RMA expression values (on the log scale) to account for batch and sex effects. Experiment Overall Design: Definition of abbreviations used in Sample records: NN = normal skin from controls; PN = uninvolved skin from cases; PP = involved skin from cases.
Chips

Affymetrix experiment GSE13433

Experiment name Transcription profiling of human alveolar soft-part sarcoma (ASPS) [GSE13433]
Source GEO
Experiment description Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study. Experiment Overall Design: For seven patients with confirmed primary or metastatic ASPS, RNA samples were isolated immediately following surgery, reverse transcribed to cDNA and each sample hybridized to duplicate high-density human U133 plus 2.0 microarrays. Array data was then analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome. Subsequent gene ontology analysis was used to identify transcripts with therapeutic or diagnostic potential. A subset of the most interesting genes was then validated using quantitative RT-PCR and immunohistochemistry.
Chips

Affymetrix experiment GSE13985

Experiment name Transcription profiling of human familial hypercholesterolemia identifies atherosclerotic markers in human blood [GSE13985]
Source GEO
Experiment description Atherosclerosis is characterized by thickening of the arterial wall and is the primary cause of the coronary artery disease and cerebrovascular disease, two of the most common causes of illness and death worldwide. One of the leading risk factors for development of atherosclerosis is familial hypercholesterolemia. Familial hypercholesterolemia is an autosomal dominant disorder, which is caused by mutations mainly located in the low-density lipoprotein receptor (LDLR) gene. It is characterized by elevated levels of low-density lipoprotein cholesterol, the presence of tendon xanthomas, and premature cardiovascular disease. Aim of this study was to find atherosclerotic markers in white blood cells of patients compared to healthy controls. None of these patients exhibited symptoms of atherosclerosis by standard diagnostic methods; however, transcriptome analysis of blood RNA indicated changes in ubiquitin proteolysis and cell adhesion system as expected in initiation steps of atherosclerosis. Experiment Overall Design: Five patients diagnosed with Familial hypercholesterolemia and five age, sex, BMI and smoking status matched controls contributed blood from which total RNA from white blood cells was isolated. RNA samples were analyzed using Affymetrix microarrays and two groups were compared for differentially expressed genes.
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Affymetrix experiment GSE15431

Experiment name Transcription profiling of human fetal testis and ovary [GSE15431]
Source GEO
Experiment description This study describes a temporal profile of gene expression from normal human fetal testes and ovaries. Gonads from 34 fetuses between 9 weeks and 20 weeks of gestation were obtained from the Department of Pathology and the Birth Defects Research Laboratory at the University of Washington. Relative transcript levels were determined using the Affymetrix Human Genome U133A Plus 2.0 arrays. Sex determination occurs in the human gonad at approximately 6 weeks; gestation with development of the testis driven by expression of SRY. In this study, SRY transcript was present and elevated at 9 weeks gestation in the testis but absent in the ovary. The transcript levels of other testis-specific factors SOX9, AMH, and the steroidogenic genes CYP17a1, CYP11a1, STAR and HSD17 3 were all significantly higher in the testis. In contrast, transcripts known to be involved in meiosis including STRA8, SPO11, SYCP3, TEX11, TEX14 and STAG3 showed highest expression in the fetal ovary beginning at week 12. These gene expression profiles will be a resource for understanding and defining normal gonad development and provide the opportunity to dissect abnormal development. Experiment Overall Design: Gonads from 34 fetuses between 9 weeks and 20 weeks of gestation were obtained, total RNA was extracted and hybridized to Affymetrix microarrays.
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Affymetrix experiment GSE16028

Experiment name Transcription profiling of human blood healthy individuals, longitudinal studies [GSE16028]
Source GEO
Experiment description The gene expression profile of blood drawn from healthy individuals was studied over a period of six months, at five time points. The gene expression profiles appeared to be constant over one month and to slightly vary over three months. A small proportion of genes were found to be differentially regulated according to gender. Differential gene regulation by age (in subjects 25-55 years of age versus subjects > 55 years of age) was not observed. Experiment Overall Design: Healthy subjects were enrolled at a single site, their health status was determined by medical history, physical examination, and standard laboratory test values. Venous blood was drawn in the morning, from fasted subjects at five time points (Day1, Day14, Day28, Day 90 and Day 180). Blood was collected into PAXgene tubes (Becton-Dickinson Diagnostics; Hombrechtikon, Switzerland).
Chips

Affymetrix experiment GSE17951

Experiment name Transcription profiling of prostate cancer samples using Affymetrix U133Plus2 array [GSE17951]
Source GEO
Experiment description Over one million prostate biopsies are performed in the U.S. every year. However, pathology examination is not definitive in a significant percentage of cases due limited diagnostic tumor. We have observed that the microenvironment of prostate tumor cells exhibits numerous differential gene expression changes and have asked whether such information can be used to distinguish tumor from nontumor . We initially compared expression analysis data (Affymetrix U133plus2) from 18 volunteer biopsy specimens to 17 specimens containing largely tumor-adjacent stroma and identified 964 significant (p_adj < 0.01 and B > 0) expression changes. These genes were filtered to eliminate possible aging-related genes and genes expressed in tumor cells > 10% of the stroma cell expression level leading to 23 candidate genes (28 Affymetrix probe sets). A classifier based on the 28 probe sets was tested on 289 independent cases, including 195 tumor-bearing cases, 99 nontumor cases (normal biopsies, normal autopsies, remote stroma as well as pure tumor adjacent stroma) all with accuracies >85%, sensitivities >90% and specificities >85%. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for categorization as tumor and nontumor . For inquires please contact dmercola@uci.edu. Experiment Overall Design: Prostate cancer gene expression profiles were studied in this project. Total RNA from 154 prostate sample with various amount of different cell types were hybridized to Affymetrix U133Plus2 array. The percentage of different cell types were determined by a pathologist.
Chips

Affymetrix experiment GSE19667

Experiment name Threshold of Biologic Response of the Small Airway Epithelium to Low Levels of Tobacco Smoke [GSE19667]
Source GEO
Experiment description Background: Healthy individuals exposed to low levels of cigarette smoke have a decrement in lung function and higher risk for lung disease compared to unexposed individuals. We hypothesized that healthy individuals exposed to low levels of tobacco smoke must have biologic changes in the small airway epithelium compared to healthy unexposed individuals. Methods: Small airway epithelium was obtained by bronchoscopy from 121 individuals; microarrays assessed genome wide gene expression, and urine nicotine and cotinine were used to categorized subjects as nonsmokers, active smokers, and low exposure. The gene expression data was used to determine the threshold and ID50 of urine nicotine and cotinine at which the small airway epithelium showed abnormal responses. Results: There was no threshold of urine nicotine without an abnormal small airway epithelial response, and only a slightly above detectable threshold abnormal response for cotinine. The nicotine ID50 for nicotine was 25 ng/ml and cotinine 104 ng/ml. Conclusions: The small airway epithelium detects and responds to low levels of tobacco smoke with transcriptome modifications. This provides biologic correlates of epidemiologic studies linking low level tobacco smoke exposure to lung health risk, health, identifies genes in the lung cells most sensitive to tobacco smoke and defines thresholds at the lung epithelium responds to inhaled tobacco smoke. Affymetrix arrays were used to assess the gene expression data of smoking-responsive genes in the in small airway epithelium obtained by fiberoptic bronchoscopy of 48 healthy non-smokers (non-smoker or Nsaets), 65 healthy smokers (smoker), 7 symptomatic smokers (SYMs) and a healthy occasional smoker (OcSs). YSB and LO contributed equally to the study.
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Affymetrix experiment GSE20711

Experiment name Epigenetic portraits of human breast cancers (expression data) [GSE20711]
Source GEO
Experiment description Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Here we used the Infinium Methylation Platform to profile at single-CpG resolution (over 14,000 genes interrogated) the methylomes of 119 breast tumours. It emerges that many genes whose expression is linked to the ER status are epigenetically controlled (or/ we show that the two major phenotypes of breast cancers determined by ER status are widely involving epigenetic regulatory mechanisms), offering the prospect of a novel approach to treating ER-positive tumours. We have distinguished methylation-profile-based tumour clusters, some coinciding with known "expression subtypes" but also new entities that may provide a meaningful basis for refining breast tumour typology. We show that methylation patterns may reflect the cellular origins of tumours. Having highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, we show that a set of immune genes have high prognostic value in specific tumour categories. By laying the ground for better understanding of breast cancer heterogeneity and improved tumour taxonomy, the precise epigenetic portraits drawn here should contribute to better management of breast cancer patients. 92 bgene expression profiling reast cancer patients. Study of epigenetic variation (methylation) linked to gene expression. No replicate, no reference sample. Two samples (Breast tumor from patient P_64 and Normal breast tissue N6) were of poor quality and were not processed for a final of 90 gene expression Samples.
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Affymetrix experiment GSE21422

Experiment name Expression profiling of human DCIS and invasive ductal breast carcinoma [GSE21422]
Source GEO
Experiment description Human healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas. Using this approach, we were able to identify a set of genes which might allow a better detection of DCIS and invasive carcinomas in the future. 5 healthy tissue samples, 9 DCIS and 5 invasive ductal carcinomas were analysed.
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Affymetrix experiment GSE23906

Experiment name Evaluation of gene expression data generated from expired Affymetrix GeneChip__ microarrays using MAQC reference RNA samples [GSE23906]
Source GEO
Experiment description The Affymetrix GeneChipR system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip____ microarrays unprocessed before their manufacturer's expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer's expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80 C, were stable over a time frame of at least four years. The new gene expression data were generated with 12 microarrays (2 types of microarrays x 2 samples x 3 replicates). Three replicates for each of the two MAQC samples (A = Stratagene's Universal Human Reference RNA; B = Ambion's Human Brain Reference RNA) were profiled in 2009 by using both the expired U133A microarrays (expired in 2004) and the unexpired U133Plus2 microarrays. In addition, gene expression data generated with unexpired U133Plus2 microarrays (AFX), other microarray platforms, and TaqManR assays by the MAQC project in 2005 were used as references to assess the stability of the MAQC samples stored at -80 C for four years by comparing new microarray data with those obtained four years ago. The MAQC reference data also allowed for further evaluation of the usefulness of the data generated with expired U133A microarrays.
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Affymetrix experiment GSE3061

Experiment name Transcription profiling of human Stratagene Universal RNA on Affymetrix U133 Plus 2.0 and U133 A Chips [GSE3061]
Source GEO
Experiment description Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Experiment Overall Design: Stratagene universal human RNA was processed using 5 aliquots of 2 ug each. The samples were hybridized to both 133 Plus 2.0 and 133 A arrays.
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Affymetrix experiment GSE31448

Experiment name Down-regulation of ECRG4, a candidate tumor suppressor gene in human breast cancer [GSE31448]
Source GEO
Experiment description ECRG4 is a promising tumor suppressor gene (TSG) recently identified in esophageal carcinoma. Its expression and prognostic value have never been explored in breast cancer. Using DNA microarray, we examined ECRG4 mRNA expression in 353 invasive breast cancer samples. A meta-analysis was performed on a large public retrospective gene expression dataset (n=1,387) to analyze correlation between ECRG4 expression and histo-clinical features including survival. To determine ECRG4 mRNA expression in breast cancer and normal breast, we first analyzed gene expression data generated by our laboratory (Institut Paoli Calmettes (IPC), Marseille, France) from cancer and normal mammary samples. Tumor tissues were from 353 patients with invasive adenocarcinoma who underwent initial surgery at IPC between 1987 and 2007. The study was approved by our institutional review board. Each patient gave a written informed consent for research use. Samples were macrodissected and frozen in liquid nitrogen within 30 min of surgical removal. All profiled specimens contained more than 60% of cancer cells (as assessed before RNA extraction using frozen sections adjacent to the profiled samples). After surgery, patients received an adjuvant multimodal treatment according to standard guidelines. Extraction of nucleic acids from frozen samples was done by using guanidium isothiocynanate and cesium chloride gradient. Expression profiles had been established for these 353 cancers pools with Affymetrix U133 Plus 2.0 human microarrays (Affymetrix__, Santa Clara, CA, USA).
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Affymetrix experiment GSE3218

Experiment name Transcription profiling of human adult male germ cell tumours [GSE3218]
Source GEO
Experiment description Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to:; 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014); 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma. ONGOING:; 4) Identification of genes associated with patient outcome and cisplatin resistance. Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 1999. The tumor samples consist of 17 seminomas, 15 pure EC, 15 pure T, 10 pure YS, 2 pure CC, and 42 NSGCT with mixed histologies. There were six patients who had each had two tumors per patient that were included in this study (designated with the same number but different letter- e.g. 155A and 155C are from same patient but represent two different tumors, one being the primary testicular lesion, the other being a liver metastasis). Five normal testis specimens (and one pooled sample consisting of equal amounts of the 5 normal testis specimens) from individual of similar ages were used as controls.
Chips

Affymetrix experiment GSE32887

Experiment name Molecular profiling and gene expression analysis in cutaneous sarcoidosis (CS) [GSE32887]
Source GEO
Experiment description Cutaneous sarcoidosis skin provides relatively non invasive access to granulomatous sarcoidosis tissue. Twenty participants were enrolled: 15 with active CS and 5 healthy volunteers. Microarray analyses comparing non-LS and healthy volunteer skin with LS showed several thousand genes differentially expressed
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Affymetrix experiment GSE3744

Experiment name Transcription profiling of 47 human breast tumor cases [GSE3744]
Source GEO
Experiment description Gene expression for 47 human breast tumor cases (normalized by GCRMA for global expression analysis)
Chips

Affymetrix experiment GSE5281

Experiment name Transcription profiling of human Alzheimers disease and the normal aged brain [GSE5281]
Source GEO
Experiment description Information about the genes that are preferentially expressed during the course of Alzheimer s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects. Aim 1. Collect brain samples from three Alzheimer s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels. Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology. We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.
Chips

Affymetrix experiment GSE6872

Experiment name Transcription profiling of human sperm from normospermic (normally fertile) and teratozoospermic individuals [GSE6872]
Source GEO
Experiment description Normal human spermatogenesis concludes with the formation of large numbers of morphologically well developed spermatozoa. While transcriptionally quiescent these cells carry an RNA payload that reflects the final spermiogenic phase of transcription. We report here the spermatozoal transcript profiles characteristic of normally fertile individuals and infertile males suffering from a consistent and severe teratozoospermia in which under 4% of spermatozoa are morphologically normal. RNA was extracted from the purified sperm cells of ejaculate and hybridized to Affymetrix U133 (v2) Microarrays. Spermatozoal RNAs were prepared from the semen samples of 21 individuals. An asymmetric dual block design was adopted with biological replicates in both blocks. 13 semen samples were assessed from normally fertile males who had fathered at least one child. 8 semen samples were assessed from infertile individuals with a severe and consistent heterogeneous teratozoospermia who showed no other abnormal semen parameters.
Chips

Affymetrix experiment GSE6883

Experiment name Transcription profiling of human normal, non-tumorigenic breast cancer cells and CD44+CD24-/low tumorigenic breast cancer cells to generate a invasiveness [GSE6883]
Source GEO
Experiment description Breast cancers contain a minority population of cancer cells characterized by CD44 expression but low or undetectable levels of CD24 (CD44+CD24-/low) that have higher tumorigenic capacity than other subtypes of cancer cells. METHODS: We compared the gene-expression profile of CD44+CD24-/low tumorigenic breast-cancer cells with that of normal breast epithelium. Differentially expressed genes were used to generate a 186-gene invasiveness gene signature (IGS), which was evaluated for its association with overall survival and metastasis-free survival in patients with breast cancer or other types of cancer. RESULTS: There was a significant association between the IGS and both overall and metastasis-free survival (P<0.001, for both) in patients with breast cancer, which was independent of established clinical and pathological variables. When combined with the prognostic criteria of the National Institutes of Health, the IGS was used to stratify patients with high-risk early breast cancer into prognostic categories (good or poor); among patients with a good prognosis, the 10-year rate of metastasis-free survival was 81%, and among those with a poor prognosis, it was 57%. The IGS was also associated with the prognosis in medulloblastoma (P=0.004), lung cancer (P=0.03), and prostate cancer (P=0.01). The prognostic power of the IGS was increased when combined with the wound-response (WR) signature. CONCLUSIONS: The IGS is strongly associated with metastasis-free survival and overall survival for four different types of tumors. This genetic signature of tumorigenic breast-cancer cells was even more strongly associated with clinical outcomes when combined with the WR signature in breast cancer. Expression profling was performed on 6 tumorigenic, 3 non tumorigenic samples of breast tumors and 3 normal breast samples on two different platforms GPL96 and GPL97. A gene signature was derived by comparing the gene expressions of 6 tumorigenic samples with 3 normal breast samples.
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Affymetrix experiment GSE7307

Experiment name Transcription profiling of a panel of 677 samples of normal and diseased human tissues [GSE7307]
Source GEO
Experiment description Normal and diseased human tissues were profiled for gene expression using the Affymetrix U133 plus 2.0 array; In total 677 samples were processed , representing over 90 distinct tissue types; Some tissue samples were purchased from Stratagene (SG), Ambion (AB), and Becton-Dickinson (BD) Experiment Overall Design: Affymetrix human U133 plus 2.0 array was used to transcriptionally profile both normal and diseased human tissues representing over 90 distinct tissue types.
Chips

Affymetrix experiment GSE7808

Experiment name Transcription profiling of human epididymis [GSE7808]
Source GEO
Experiment description Analysis of the gene expression pattern in the caput, corpus and cauda epididymides of three donors of 26-50 years of age with no medical pathologies that could affect reproductive function. The data generated in this study demonstrate a region specific gene expression pattern along the human epididymis that seems to coincide with the morphological distinctive features of the excurrent duct. Experiment Overall Design: Epididymides were dissected in caput, corpus and cauda epididymidis from three donors: ages 26, 47, and 50 yrs. Expression profiles were generated on Affymetrix GeneChip U133 Plus 2.0 arrays (9 samples total).
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Affymetrix experiment GSE803

Experiment name Transcription profiling of human normal tissue [GSE803]
Source GEO
Experiment description Normal human tissue expression profiling
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Affymetrix experiment GSE8764

Experiment name Transcription profiling of human parotid gland gene expression to determine age and gender related changes [GSE8764]
Source GEO
Experiment description Previous studies suggest that there may be age and gender related differences in salivary gland function. However, the limited and often conflicting information available from healthy populations makes it difficult to confirm these differences. The purpose of the present study was to evaluate and compare changes in gene expression associated with age and gender in the human parotid gland. Differential expression, defined as statistically significant differences with at least 1.5 fold changes, was detected using the Affymetrix GeneChip HGU133plus2.0 microarray in 787 gene probe sets; 320 showed higher expression in males, while 467 showed higher expression in females. Several genes associated with saliva secretion were differentially expressed in male and female parotid gland including vesicle-associated membrane protein 3 VAMP3, synaptosomal-associated protein SNAP23, RAS oncogene family member RAB1A, syntaxin binding protein STXBP1. When the gene expression results from the youngest (19-38 years old) and the oldest (65-69 years old) female subjects were further evaluated, it was found that the expression of 228 genes were altered during aging; 155 genes were down-regulated, whereas 73 genes were up-regulated in the female parotid gland. Of the genes that were altered during aging, 24 of the 28 genes (86%) classified as being associated with immune responses were down-regulated in the aged parotid gland. A panel of differentially expressed, age- and gender-related genes was selected for further study by quantitative, real-time RT-PCR. Comparable differences in gene expression were detected by both Affymetrix array and quantitative, real-time RT-PCR methods. Taken together, our data suggest that salivary gland function may be adversely affected in the aged population due, at least in part, to the down regulation of several categories of genes. Moreover, the gender specific gene expressions identified in the present study correlates with the previously observed sexual dimorphism in salivary gland function. Experiment Overall Design: Human parotid glands were obtained from healthy male and female subjects (19-85 years of age). 3 young female parotid glands were compared with 3 older female parotid gland. 8 Female samples were compared with 5 male samples
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Hide | TopExpressed Sequence tags

EST library 1042

Library name Soares_NFL_T_GBC_S1 [1042]
Source Unigene
Library description Equal amounts of plasmid DNA from three normalized libraries (fetal lung NbHL19W, testis NHT, and B-cell NCI_CGAP_GCB1) were mixed, and ss circles were made in vitro. Following HAP purification, this DNA was used as tracer in a subtractive hybridization reaction. The driver was PCR-amplified cDNAs from pools of 5,000 clones made from the same 3 libraries. The pools consisted of I.M.A.G.E. clones 297480-302087, 682632-687239, 726408-728711, and 729096-731399. Subtraction by Bento Soares and M. Fatima Bonaldo.
Annotation by Bgee curatorsAnatomical structure ID: EV:0100000 - Developmental stage ID: HsapDO:0000037
EST

EST library 16264

Library name Full Length cDNA from the Mammalian Gene Collection [16264]
Source Unigene
Library description The ORFs were PCR amplified from the MGC (Mammalian Gene Collection) and cloned by recombinational Gateway cloning into pDONR223 Donor vector. Reference : MGC (Mammalian Gene Collection) Program Team, Generation and Initial Analysis of more than 15,000 Full-Length Human and Mouse cDNA Sequences. PNAS, 2002, 99(26), 16899-16903
Annotation by Bgee curatorsAnatomical structure ID: EV:0100000 - Developmental stage ID: HsapDO:0000044
EST

EST library 16441

Library name Sugano cDNA library, testis [16441]
Source Unigene
Library description
Annotation by Bgee curatorsAnatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000044
EST

EST library 18416

Library name LIVER2 [18416]
Source Unigene
Library description
Annotation by Bgee curatorsAnatomical structure ID: EV:0100089 - Developmental stage ID: HsapDO:0000044
EST

EST library 18476

Library name TESTI2 [18476]
Source Unigene
Library description
Annotation by Bgee curatorsAnatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000044
EST

EST library 249

Library name Stratagene lung (#937210) [249]
Source Unigene
Library description Cloned unidirectionally. Primer: Oligo dT. normal lung. Average insert size: 1.0 kb; Uni-ZAP XR Vector; ~5' adaptor sequence: 5' GAATTCGGCACGAG 3' ~3' adaptor sequence: 5' CTCGAGTTTTTTTTTTTTTTTTTT 3'
Annotation by Bgee curatorsAnatomical structure ID: EV:0100042 - Developmental stage ID: HsapDO:0000166
EST

EST library 628

Library name Soares_testis_NHT [628]
Source Unigene
Library description 1st strand cDNA was prepared from mRNA obtained from Clontech Laboratories, Inc., and primed with a Not I - oligo(dT) primer [5' TGTTACCAATCTGAAGTGGGAGCGGCCGCCCAATTTTTTTTTTTTTTTTT 3']. Double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia), digested with Not I and cloned into the Not I and Eco RI sites of the modified pT7T3 vector. Library went through one round of normalization to Cot5, and was constructed by Bento Soares and M. Fatima Bonaldo.
Annotation by Bgee curatorsAnatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000044
EST

EST library 843

Library name Soares_total_fetus_Nb2HF8_9w [843]
Source Unigene
Library description 1st strand cDNA was prepared from mRNA obtained from pooled 8-9 week (total) fetus material with a Not I - oligo(dT) primer [5' TGTTACCAATCTGAAGTGGGAGCGGCCGCTTAATTTTTTTTTTTTTTTTT 3']. Double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia), digested with Not I and cloned into the Not I and Eco RI sites of the modified pT7T3 vector. Library went through one round of normalization, and was constructed by Bento Soares and M. Fatima Bonaldo.
Annotation by Bgee curatorsAnatomical structure ID: EHDAA:38 - Developmental stage ID: HsapDO:0000197
EST

EST library 8571

Library name NIH_MGC_97 [8571]
Source Unigene
Library description Oligo-dT primed using primer 5'-TTTTTTTTTTTTTTTTVN-3', size-selected for average insert size 2.2 kb and normalized to ROT 5. This is a primary library enriched for full-length clones and constructed using the Cap-trapper method (Carninci, in preparation). Library constructed by M. Brownstein (NIMH/NHGRI, National Institutes of Health). Note: this is a NIH_MGC Library.
Annotation by Bgee curatorsAnatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000044
EST

EST library 9725

Library name NIH_MGC_119 [9725]
Source Unigene
Library description RNA source normal medulla from anonymous male age 27. Library is oligo-dT primed and directionally cloned (EcoRV site is destroyed upon cloning). Average insert size 1.3 kb, insert size range 0.9-3 kb. Library is normalized and enriched for full-length clones and was constructed by C. Gruber (Invitrogen). Research Genetics tracking code 013. Note: this is a NIH_MGC Library.
Annotation by Bgee curatorsAnatomical structure ID: EV:0100275 - Developmental stage ID: HsapDO:0000121
EST