Bgee: Gene Expression Evolution

Expression data retrieved for the gene ENSG00000115297: TLX2 - Homo sapiens

Query parameters
Gene: ENSG00000115297 - TLX2
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: GSM752692 - log2 RPK threshold: -3.019 - Annotation by Bgee curators: Anatomical structure ID: EV:0100167 - Developmental stage ID: HsapDO:0000157
    • Gene ID: ENSG00000115297 - log2 RPK score: -2.966 - Detection flag: present - Quality: high quality
  • Sample ID: GSM752707 - log2 RPK threshold: -4.615 - Annotation by Bgee curators: Anatomical structure ID: EV:0100102 - Developmental stage ID: HsapDO:0000121
    • Gene ID: ENSG00000115297 - log2 RPK score: -1.644 - 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: ENSG00000115297 - log2 RPK score: 0.426 - Detection flag: present - Quality: high quality

Hide | TopAffymetrix

Affymetrix experiment E-MEXP-3111

Experiment name Interactome of Human Embryo Implantation: Identification of Gene Expression Pathways, Regulation, and Integrated Regulatory Networks. [E-MEXP-3111]
Source ArrayExpress
Experiment description Possible interactions between endometrium and implanting embryo in humans
Chips
  • Chip ID: SA_27 - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA_19 - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA_22 - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA_20 - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA03_K24 - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA01_K22F - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA02_K18F - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: SA04_mix - Annotation by Bgee curators: Anatomical structure ID: EV:0100115 - Developmental stage ID: HsapDO:0000088
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - 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_Plate_3_A1 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000140
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - 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: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 146139hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: absent - Quality: high quality
  • Chip ID: 153175hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151990hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - 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: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151992hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153574hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153176hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000160
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 152392hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - 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: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153181hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000136
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 152393hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153178hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000142
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151988hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151989hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 151994hp133a11 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000163
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality
  • Chip ID: 153578hp133a21 - Annotation by Bgee curators: Anatomical structure ID: EV:0100047 - Developmental stage ID: HsapDO:0000140
    • Probeset ID: 211049_at - Mapped to gene: ENSG00000115297 - 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: 211049_at - Mapped to gene: ENSG00000115297 - Detection flag: marginal - Quality: low quality

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 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 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 GSE13564

Experiment name Transcription profiling of human prefrontal cortex during postnatal development [GSE13564]
Source GEO
Experiment description Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing. PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex Experiment Overall Design: The dataset consists of 44 individuals varying in age from 0 to 49 years
Chips

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.
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 GSE18140

Experiment name COX-2 network as predictive molecular marker for clinical pregnancy in IVF [GSE18140]
Source GEO
Experiment description CONTEXT Nowadays, the molecular mechanisms involved in endometrial receptivity and implantation are still not clear. OBJECTIVE The gene expression of human endometrium of patients undergoing an IVF treatment with GnRH antagonists/rec-FSH was studied. CONCLUSIONS COX-2 has been extensively studied as a crucial fertility element in both knock-out mice and human. It appears that increased expression of COX-2 and/or SCGB1D2 on the day of oocyte retrieval in GnRH antagonist/rec-FSH stimulated cycles coincides with a lower probability of achieving a clinical pregnancy in this cycle. Keywords: gene expression analysis, clinical pregnancy in IVF stimulated cycles Endometrial biopsies taken from patients on day of oocyte retrieval in stimulated IVF cycles with 1 or 2 embryos replaced in the same cycle. Gene expression of pregnant patients (n=4) was compared with matched non-pregnant patients (n=4)
Chips

Affymetrix experiment GSE18897

Experiment name Transcription profiling of human whole blood from obese diet-sensitive, obese diet-resistant and lean subjects [GSE18897]
Source GEO
Experiment description We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss. Experiment Overall Design: A total of 80 samples are analyzed. This consists of 20 lean subjects studied at one timepoint and 20 obese subjects (10 diet-sensitive and 10 diet-resistant) studied at 3 timepoints during caloric restriction (day of entry into program, week 3 into the program and week 6 into the program)
Chips

Affymetrix experiment GSE20146

Experiment name Expression analysis of dissected GPi in Parkinson's disease [GSE20146]
Source GEO
Experiment description Genome-wide transcriptome analysis of expression changes in Globus Pallidus interna (GPi) from Parkinson's disease brain tissue versus control brain tissue. Post-mortem brain expression analysis performed in 10 PD brain samples and 10 control brain samples.
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Affymetrix experiment GSE26051

Experiment name Analysis of Human Tendinopathy Gene Expression [GSE26051]
Source GEO
Experiment description Chronic tendon injuries, also known as tendinopathy, are common among professional and recreational athletes. These injuries result in a significant amount of morbidity and health care expenditure and yet little is known about the molecular mechanism leading to tendinopathy. We have used histological evaluation and molecular profiling to determine the gene expression changes in 23 human patients undergoing surgical procedures for the treatment of chronic tendinopathy. Diseased tendons have altered extracellular matrix, fiber disorientation, increased cellular content and vasculature and the absence of inflammatory cells. Global gene expression profiling identified 1783 transcripts with significant different expression patterns in the diseased tendons. Global pathway analysis further suggests altered expression of extracellular matrix proteins and the lack of an appreciable inflammatory response. We have identified pathways and genes regulated in tendinopathy samples that will help contribute to the understanding of the disease towards the development of novel therapeutics. A prospective study was initiated to collect tissue from patients undergoing surgery as standard of care for tendinopathy. Biopsies (~3mm^3) of diseased tendons as well as a section of grossly normal appearing tendon were collected from 23 patients. Written informed consent was obtained from all patients prior to any study related procedure.
Chips

Affymetrix experiment GSE27505

Experiment name Prospective Identification, Isolation, and Profiling of a Telomerase-Expressing Subpopulation of Human Neural Stem Cells, using sox2 Enhancer-Directed Fluorescence-Activated Cell Sorting [GSE27505]
Source GEO
Experiment description Sox2 is expressed by neural stem and progenitor cells, and a sox2 enhancer identifies these cells in the forebrains of both fetal and adult transgenic mouse reporters. We found that an adenovirus encoding EGFP placed under the regulatory control of a 0.4 kb sox2 core enhancer selectively identified multipotential and self-renewing neural progenitor cells in dissociates of human fetal forebrain. Gene expression analysis of E/sox2:EGFP-sorted neural progenitor cells, normalized to the unsorted forebrain dissociates from which they derived, revealed marked overexpression of genes within the notch and wnt pathways, and identified multiple elements of each pathway that appear selective to human neural progenitors. We used adenoviral E/sox2:EGFP to transduce dissociates of the second trimester human ventricular zone (VZ)/ subventricular zone (SVZ), followed by EGFP-directed fluorescence-activated cell sorting (FACS). The sox2 isolates and unsorted controls from different gestational ages (16-19 wks, n=4) were then subject to RNA extraction and hybridization on Affymetrix microarrays.
Chips

Affymetrix experiment GSE28160

Experiment name Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-Associated Neurocognitive Disorders [GSE28160]
Source GEO
Experiment description Antiretroviral therapy (ART) has reduced morbidity and mortality in HIV infection; however HIV-1-associated neurocognitive disorders (HAND) persist despite treatment. We used microarray analysis in post-mortem brain tissues to determine ART effectiveness in the brain and to identify molecular signatures of HAND under ART. We performed microarray analysis using Affymetrix Arrays in portmortem brain tissues from seven treated and eight untreated HAND patients and six uninfected controls.
Chips

Affymetrix experiment GSE28750

Experiment name Development and Validation of a Novel Molecular Biomarker Diagnostic Test for the Early Detection of Sepsis [GSE28750]
Source GEO
Experiment description Introduction: Sepsis is a complex immunological response to infection characterized by early hyperinflammation followed by severe and protracted immunosuppression, suggesting that a multi-marker approach has the greatest clinical utility for early detection, within a clinical environment focused on SIRS differentiation. Pre-clinical research using an equine sepsis model identified a panel of gene expression biomarkers that define the early aberrant immune activation. Thus, the primary objective was to apply these gene expression biomarkers to distinguish patients with sepsis from those who had undergone major open surgery and had clinical outcomes consistent with systemic inflammation due to physical trauma and wound healing. Methods: This was a multi-centre, prospective clinical trial conducted across 4 tertiary critical care settings in Australia. Sepsis patients were recruited if they met the 1992 Consensus Statement criteria and had clinical evidence of systemic infection based on microbiology diagnoses (n=27). Participants in the post-surgical (PS) group were recruited pre-operatively and blood samples collected within 24 hours following surgery (n=38). Healthy controls (HC) included hospital staff with no known concurrent illnesses (n=20). Each participant had minimally 5ml of PAXgene blood collected for leucocyte RNA isolation and gene expression analyses. Affymetrix array and multiplex tandem (MT)-PCR studies were conducted to evaluate transcriptional profiles in circulating white blood cells applying a set of 42 molecular markers that had been identified a priori. A LogitBoost algorithm was used to create a machine learning diagnostic rule to predict sepsis outcomes. Results: Based on preliminary microarray analyses comparing HC and sepsis groups. A panel of 42-gene expression markers were identified that represented key innate and adaptive immune function, cell cycling, WBC differentiation, extracellular remodelling and immune modulation pathways. Comparisons against GEO data confirmed the definitive separation of the sepsis cohort. Quantitative PCR results suggest the capacity for this test to differentiate severe systemic inflammation from HC is 92%. AUC ROC curve findings demonstrated sepsis prediction within a mixed inflammatory population, was between 86 - 92%. Conclusions: This novel molecular biomarker test has a clinically relevant sensitivity and specificity profile, and has the capacity for early detection of sepsis via the monitoring of critical care patients. GEO Note: Data made available represents the preliminary microarray investigation performed on Human U133 Plus 2.0 GeneChips (Affymetrix), assaying 41 patient samples (Sepsis n=10, Post-Surgical n=11, Control n=20). This was a multi-centre, prospective clinical trial conducted across 4 tertiary critical care settings in Australia. Sepsis patients were recruited if they met the 1992 Consensus Statement criteria and had clinical evidence of systemic infection based on microbiology diagnoses (n=27). Participants in the post-surgical (PS) group were recruited pre-operatively and blood samples collected within 24 hours following surgery (n=38). Healthy controls (HC) included hospital staff with no known concurrent illnesses (n=20). Each participant had minimally 5ml of PAXgene blood collected for leucocyte RNA isolation and gene expression analyses. The GEO data represents the preliminary microarray investigation performed on Human U133 Plus 2.0 GeneChips (Affymetrix), assaying 41 patient samples (Sepsis n=10, Post-Surgical n=11, Control n=20).
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Affymetrix experiment GSE29832

Experiment name Expression data from pure/mixed blood and breast to test feasability of deconvolution of clinical samples [GSE29832]
Source GEO
Experiment description Samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Blood, for example, contains many different cell types that are derived from a distinct lineage and carry out a different immunological purpose. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies. We used microarrays to detail a statistical approach to model expression from a mixed cell population as the weighted average of expression from different cell types. Consequently, we can accurately and efficiently estimate the abundance of various cell populations. Favoring computation over manual purification has its advantages, such as measuring responses of multiple cell types simultaneously, keeping samples intact, and identifying biologically relevant differentially expressed genes. We mixed breast and blood biospecimens derived from female adults at the cRNA homogenate level in different proportions. Data was RMA normalized.
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Affymetrix experiment GSE29981

Experiment name Expression data from human endometrium [GSE29981]
Source GEO
Experiment description The purpose of this study was to compare and contrast the expression of mRNA sequences in samples of endometrial glandular epithelium taken at discrete points in the menstrual cycle of healthy female subjects. This study was approved by the Erasme Hospital Ethics Committee and was conducted at the Pfizer Clinical Research Unit at the Erasme hospital, Brussels. The study was conducted in accordance with the Declaration of Helsinki on Ethical Principals for Medical Research Involving Human Subjects, adopted by the General Assembly of the World Medical Association (1996). In addition, the study was conducted in accordance with the protocol, the principles of the International Conference on Harmonization guideline on Good Clinical Practice and applicable local regulatory requirements and laws. Written informed consent was obtained from all participants in this study prior to screen. Female healthy subjects were between 20 and 39 years of age and had a regular menstrual cycle. A total of 23 endometrial biopsies were taken from women at different stages of their menstrual cycle (mid & late follicular; early & mid luteal phases) by pipelle catheter. Glandular epithelium was laser capture microdissected and total RNA was purified, labelled and hybridized to Affymetrix HG-U133 Plus 2 chips using standard protocols. The resulting data were subjected to a principal component analysis and assessment by a proprietary methodology, the causal reasoning engine. Using this analysis we describe new progesterone marker genes and a robust methodology which may be useful for identifying endometrial pharmacological response genes or diagnostic disease markers. A single sample was taken from each of 20 human subjects at time points across the menstrual cycle.
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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 GSE4488

Experiment name Transcription profiling of blood from human pituitary adenoma predisposition (PAP) patients to characterize the genetic basis of low penetrance tumor susceptibility [GSE4488]
Source GEO
Experiment description While identification of genes mutated in high penetrance tumor predisposition syndromes has been a success story, much less progress has been made in characterizing the genetic basis of low penetrance tumor susceptibility. Combining recently introduced chip-based technologies with traditional genealogy work we have identified inactivating germline mutations in patients with pituitary adenoma predisposition (PAP). To identify the PAP locus whole genome SNP genotyping and linkage analysis was combined with gene expression profiling from 16 individuals (9 affected/obligatory carriers: A2, A6, A8, A14, A16, A18, A20, A21, A22, and 7 controls). Statistical analysis was performed on probe sets mapped to the linked region. The experiment consisted of a collection of blood samples from identified families where PAP was observed and analysis of gene expression data used together with SNP genoptyping and linkage analysis. The findings were further studied using direct screening and other supporting methods.
Chips

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.
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Hide | TopExpressed Sequence tags

EST library 10290

Library name UI-E-EJ0 [10290]
Source Unigene
Library description UI-E-EJ0 is a subtracted cDNA library constructed according to Bonaldo, Lennon and Soares, Genome Research, 6:791-806, 1996. First strand cDNA synthesis was primed with an oligo-dT primer containing a Not I site. Double stranded cDNA was ligated to an EcoR I adaptor, digested with Not I, and cloned directionally into pT7T3-Pac vector. The oligonucleotide used to prime the synthesis of first-strand cDNA contains a library tag sequence that is located between the Not I site and the (dT)18 tail. The sequence tags for this library are: fetal eyes, AGAATCAAGA; lens, CGATTAGCGA; eye anterior segment, AATGCCGCAT; optic nerve, CCATTAAGTG; retina, CCGCG; Retina Foveal and Macular, GTCC; RPE and Choroid, ACCTA. This library was created for the program, Gene Discovery in the Visual System, supported by National Eye Institute (NEI).
Annotation by Bgee curatorsAnatomical structure ID: EV:0100336 - Developmental stage ID: HsapDO:0000001
EST

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 910

Library name NCI_CGAP_Pr22 [910]
Source Unigene
Library description 1st strand cDNA was prepared from normal prostate bulk tissue, and was then primed with a Not I - oligo(dT) primer. 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 is normalized, and was constructed by Bento Soares and M. Fatima Bonaldo.
Annotation by Bgee curatorsAnatomical structure ID: EV:0100104 - Developmental stage ID: HsapDO:0000044
EST