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Links from GEO DataSets

Items: 20

1.
Full record GDS5277

Rheumatoid arthritis and response to anti-TNF therapy: blood

Analysis of blood from rheumatoid arthritis (RA) patients prior to anti-TNF therapy. Response of patients to anti-TNF therapy assessed after 14 weeks. Results identify a gene expression signature for predicting the response to anti-TNF therapy.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 4 other sets
Platform:
GPL570
Series:
GSE15258
86 Samples
Download data: CEL
2.

Whole blood transcript profiling of rheumatoid arthritis patients

(Submitter supplied) The whole blood was collected pre-treatment from rheumatoid arthritis patients starting the anti_TNF therapy. All patients were naïve to anti_TNFs. The disease activity was measured using the DAS28 score at the pre-treatment visit1 (DAS28_v1) and 14 weeks after treatment visit3 (DAS28_v3). The response to the therapy was evaluated using the EULAR [European League Against Rheumatism] definition of the response. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS5277
Platform:
GPL570
86 Samples
Download data: CEL
Series
Accession:
GSE15258
ID:
200015258
3.

Pharmacodynamic Biomarkers and Differential Effects of TNF- and GM-CSF-Targeting Biologics in Rheumatoid Arthritis

(Submitter supplied) A major unmet need in rheumatoid arthritis (RA) is the choice of treatment options for patients with an inadequate response to anti-TNF agents (anti-TNF–IR). In order to identify pharmacodynamic biomarkers and assess differential effects of TNF- and non–TNF-targeting agents on RA patients with an inadequate response to anti-TNF–IR in comparison with biologic-naïve patients, peripheral protein markers and gene expression levels in association with clinical response posttreatment in two disease strata were assessed in disease-modifying antirheumatic drug (DMARD)-IR and anti-TNF-IR patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
147 Samples
Download data: TXT
4.

Genome-wide transcriptional analysis of synovial tissue gene expression associated with the response to anti-TNF therapy in Rheumatoid Arthritis

(Submitter supplied) Synovial biopsies of Rheumatoid Arthritis patients with active disease were obtained prior to anti-TNF therapy. Clinical response to anti-TNF treatment was measured 20 weeks later using the EULAR response criteria. Gene expression profiles of patients responding to anti-TNF therapy were compared to non-responders and several genes were found to be differentially expressed between both groups of Rheumatoid Arthritis patients.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL8234
11 Samples
Download data: TXT
Series
Accession:
GSE47726
ID:
200047726
5.

Whole blood gene expression profiling of rheumatoid arthritis patients

(Submitter supplied) Approximately 30% of rheumatoid arthritis patients achieve inadequate response to anti-TNF biologics. In this study, we sought to identify a blood gene expression biomarker correlating with 12-week response to infliximab in patients with moderate to severe disease. Response was assessed using dynamic contrast-enhanced MRI imaging of the wrist.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10379
59 Samples
Download data: CEL
Series
Accession:
GSE58795
ID:
200058795
6.

Differential expression of rituximab responders vs. non responders on 3 different blood cell types

(Submitter supplied) New and effective therapeutical options are available for the treatment of Rheumatoid Arthritis. One of such treatments is rituximab, and chimeric anti-CD20 antibody that selectively depletes the CD20+ B cell subpopulation. Similar to established anti-TNF alpha therapies, there is a subgroup of RA patients that do not experience significant clinical response. Therefore, one of the major necessities in actual RA therapeutical management is to identify reliable predictors of the response to this therapies. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL2507
23 Samples
Download data: TXT
Series
Accession:
GSE15316
ID:
200015316
7.

Efficacy of anti-TNF biologic agent, infliximab, for RA patients using transcriptome analysis of white blood cells

(Submitter supplied) Introduction of biologics, such as infliximab, to the therapy of rheumatoid arthritis (RA) patients has revolutionized the treatment of this disease. However, biomarkers for predicting the efficacy of the drug at an early phase of treatment for selecting real responders have not been found. We here present predictive markers based on a thorough transcriptome analysis of white blood cells from RA patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
68 Samples
Download data: TXT
Series
Accession:
GSE20690
ID:
200020690
8.

RNA-sequencing of whole blood samples from biologic naïve rheumatoid arthritis patients initiating anti-TNF treatment

(Submitter supplied) Objective: use comprehensive molecular profiling to understand the molecular mechanisms that affect clinical response to anti-TNF therapy in rheumatoid arthritis (RA) and to identify predictive markers to differentiate good responders and non-responders. Methods: two independent cohorts of 40 and 36 biologic-naïve RA patients were selected from the Corrona (Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory coNditions) CERTAIN registry and categorized by EULAR response criteria. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
128 Samples
Download data: TXT
Series
Accession:
GSE129705
ID:
200129705
9.

mRNA expression profile in peripheral blood cells of RA patients following treatment with an anti-TNFa mAb, infliximab

(Submitter supplied) Objectives: We monitored the mRNA expression profiles of peripheral blood cells during treatment with a tumor necrosis factor-a inhibitor, infliximab, in patients with rheumatoid arthritis (RA). Using a DNA microarray analysis, we demonstrated a unique set of genes, with distinct baseline and post-treatment changes in expression between responders and non-responders to infliximab treatment.Methods: Using a customized low-density cDNA microarray and a reliable data collection system, we monitored the mRNA expression profiles of whole blood cells from 18 RA patients before and after the infusion of infliximab for up to 22 weeks. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL5460
72 Samples
Download data: TXT
Series
Accession:
GSE8350
ID:
200008350
10.

Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

(Submitter supplied) The aim of this study was to identify the specific molecular biological features predicting the therapeutic outcomes of three bDMARDs, infliximab (IFX), tocilizumab (TCZ), and abatacept (ABT) by studying blood gene expression signature of patients prior to biologic treatment in a unified test platform. GSEA analyses showed that inflammasome genes were significantly upregulated in IFX’s NON-REM compared with its REM. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6480
209 Samples
Download data: TXT
Series
Accession:
GSE78068
ID:
200078068
11.

Microarray predictor of response to infliximab in rheumatoid arthritis (RA) patients

(Submitter supplied) We sought to find a gene-expression multigene predictor of response to infliximab therapy in Rheumatoid Arthritis patients. Using internal and external cross-validation systems we have built and validated an 8-gene predictor for response to infliximab.
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS3628
Platform:
GPL2507
44 Samples
Download data: TXT
Series
Accession:
GSE12051
ID:
200012051
12.
Full record GDS3628

Rheumatoid arthritis and response to anti-TNF alpha therapy: blood

Analysis of whole blood from rheumatoid arthritis patients at baseline of infliximab therapy. Infliximab is an anti-TNF alpha antibody. Clinical response to infliximab determined at week 14 of therapy. Results identify a gene expression signature for predicting the response to infliximab.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 2 disease state sets
Platform:
GPL2507
Series:
GSE12051
44 Samples
Download data: TXT
13.

Rheumatoid arthritis and anti-TNF treatment

(Submitter supplied) In 15 patients with rheumatoid arthritis the baseline expression (t=0) of type I IFN-regulated genes was determined in peripheral blood cells (PAXgene) using cDNA-microarrays and compared to levels one month after (t=1) anti-TNF treatment (infliximab). Therefore, we used 43K cDNA microarrays from the Stanford Functional Genomics Facility (http://microarray.org/sfgf/) printed on aminosilane-coated slides containing ~20.000 unique genes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL9871 GPL9870 GPL9869
30 Samples
Download data
Series
Accession:
GSE19821
ID:
200019821
14.

Random forest-based modelling to detect novel biomarkers for prostate cancer progression

(Submitter supplied) The clinical course of prostate cancer (PCa) is highly variable, demanding an individualized approach to therapy and robust prognostic markers for treatment decisions. We here present a random forest-based classification model to predict aggressive behaviour of PCa. DNA methylation changes between PCa cases with good or poor prognosis (discovery cohort with n=78) were used as input. The model was validated with data from two independent PCa cohorts from ICGC and TCGA. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL18809
70 Samples
Download data: IDAT, TXT
Series
Accession:
GSE127985
ID:
200127985
15.

The relationship between the gene expression profile in the synovium of RA patients at baseline and the clinical response to infliximab treatment

(Submitter supplied) Background: Although the use of TNF inhibitors has fundamentally changed the way rheumatoid arthritis (RA) is treated, not all patients respond well. It is desirable to facilitate the identification of responding and non-responding patients prior to treatment, not only to avoid unnecessary treatment but also for financial reasons. In this work we have investigated the transcriptional profile of synovial tissue sampled from RA patients before anti-TNF treatment with the aim to identify biomarkers predictive of response. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL7768
62 Samples
Download data: GPR
Series
Accession:
GSE21537
ID:
200021537
16.

Gene expression profiling in peripheral blood cells of patients with rheumatoid arthitis in response of anti-TNF-alpha

(Submitter supplied) The goal of this study was to characterize the effects of anti-TNF-alpha treatments on gene expression in peripheral blood mononuclear cells. 8 women were submitted to a 12 weeks treatments with Etanercept or Adalimumab. Peripheral blood mononuclear cells were taken before and after the treatment. The samples from the same patients (obtained before and after the 12 weeks of treatment) were compared on the same microarray. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL1456
8 Samples
Download data: GPR
Series
Accession:
GSE12897
ID:
200012897
17.

Consensus Preprocessing of GEO and ArrayExpress Normal and Diseased Lung Tissue Microarray Data

(Submitter supplied) The Affymetrix oligonucleotide microarrays measure gene expression by quantifying intensity of fluorescently labeled gene fragments that bind to sets of 25-mer oligonucleotide probes on the chip with specific sequences tailored to be complementary to the target genes. Each gene is associated with a "probe set" containing several pairs (usually 11) of "perfect match" (perfectly complementary to target sequence) and "mismatch" (different base at position 13 of 25) probes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Third-party reanalysis
Download data: TXT
Series
Accession:
GSE60486
ID:
200060486
18.

MAQC-II Project: Iconix data set

(Submitter supplied) The Iconix data set (endpoint B) was provided by Iconix Biosciences, Inc. (Mountain View, CA, USA). The study objective was to assess, upon short term exposure, hepatic tumor induction bynon-genotoxic chemicals, since there are currently no accurate and well-validated short-term tests to identify non-genotoxic hepatic tumorigens, thus necessitating an expensive 2-year rodent bioassay before a risk assessment can begin. more...
Organism:
Rattus norvegicus
Type:
Third-party reanalysis; Expression profiling by array
Download data: TXT, XLS
Series
Accession:
GSE24417
ID:
200024417
19.

MAQC-II Project: NIEHS data set

(Submitter supplied) The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). more...
Organism:
Rattus norvegicus
Type:
Expression profiling by array
Platform:
GPL1355
418 Samples
Download data: CEL
Series
Accession:
GSE24363
ID:
200024363
20.

MAQC-II Project: Multiple myeloma (MM) data set

(Submitter supplied) The multiple myeloma (MM) data set (endpoints F, G, H, and I) was contributed by the Myeloma Institute for Research and Therapy at the University of Arkansas for Medical Sciences (UAMS, Little Rock, AR, USA). Gene expression profiling of highly purified bone marrow plasma cells was performed in newly diagnosed patients with MM. The training set consisted of 340 cases enrolled on total therapy 2 (TT2) and the validation set comprised 214 patients enrolled in total therapy 3 (TT3). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
559 Samples
Download data: CEL, XLS
Series
Accession:
GSE24080
ID:
200024080
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