GEO DataSets

(Submitter supplied) A gene expression profiling sub-study was conducted in which colonic biopsy samples were collected for RNA extraction and hybridization to microarrays from 48 patients with UC who were participating in ACT 1, a placebo-controlled study of infliximab. Gene expression profiles from infliximab responders were compared with those of baseline and infliximab non-responder samples. Infliximab had a significant effect on mRNA expression in treatment responders, with both infliximab dose and duration of treatment having an effect. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

113 Samples

Download data: CEL

(Submitter supplied) Infliximab, an anti-TNF-alpha monoclonal antibody, is an effective treatment for ulcerative colitis (UC) with over 60% of patients responding to treatment and up to 30% reaching remission. The mechanism of resistance to anti-TNF-alpha is unknown. This study used colonic mucosal gene expression to provide a predictive response signature for infliximab treatment in UC. Keywords: drug response

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) Infliximab, an anti-TNFa monoclonal antibody, is an effective treatment for ulcerative colitis (UC) inducing over 60% of patients to respond to treatment. Consequently, about 40% of patients do not respond. This study analyzed mucosal gene expression from patients enrolled in ACT1 to provide a predictive response signature for infliximab treatment. Keywords: predictive response signature

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

23 Samples

Download data: CEL

(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

(Submitter supplied) Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4365

Platform:

GPL570

43 Samples

Download data: CEL

Analysis of colonic biopsies from patients with histologically active or inactive UC and from healthy, non-inflammatory controls. UC is a chronic inflammatory disease with periods of active disease followed by remission. Results provide insight into molecular events associated with UC remission.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 agent, 4 disease state sets

Platform:

GPL570

Series:

GSE38713

43 Samples

Download data: CEL

(Submitter supplied) Background & Aims. As a T cell-mediated disease of the colonic epithelium, ulcerative colitis (UC) is likely to share pathogenic elements with other T cell-mediated inflammatory diseases. Recently we showed T cell-mediated rejection of kidney and heart transplants share large scale molecular changes. We hypothesized that UC would manifest a similar disturbance, and that these features would correlate with response to infliximab. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

56 Samples

Download data: CEL

(Submitter supplied) RNA sequencing was performed on RNA isolated from baseline biopsies from UC patients enrolled in the Phase II EUCALYPTUS study of etrolizumab. Gene expression differences were identified in a subset of anti-TNF naïve patients that achieved clinical remission at 10 weeks in response to etrolizumab.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

73 Samples

Download data: TAB

(Submitter supplied) Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

56 Samples

Download data: CEL

(Submitter supplied) Crohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract. We performed a whole-genome transcriptional analysis using colonic biopsies from CD patients before and after anti-TNF-α therapy.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17996

39 Samples

Download data: CEL

(Submitter supplied) Colonic Crohn's Disease from a single patient in remission with mild disease index

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: CSV

(Submitter supplied) IL23R signaling dependent genes are significantly upregulated in Crohn’s disease non-responders compared to responders during ongoing anti-TNF therapy

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

6 Samples

Download data: TXT

(Submitter supplied) Our group used rectal biopsies from patients with active ulcerative colitis (UC) and differential response to glucocorticoid treatment, to generate a predictive computational strategy based on systems biology. Contrasting mRNA and miRNAs intestinal expression profiles with updated molecular information related to UC and glucocorticoids, we were able to identify a mechanism of action (MoA) associated with corticosteroid failure in UC. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

46 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15456 GPL14951

76 Samples

Download data

(Submitter supplied) BACKGROUND: Glucocorticoid (GC) refractoriness is a common and unpredictable phenomenon in ulcerative colitis (UC). Although it has been demonstrated that NFkB is involved in its mechanism of action (MoA), there are no conclusive studies on the molecular functions involved. The current study describes in depth the MoA related to GC failure, by integrating transcriptomic data from UC patients, and updated molecular data on UC and GC. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15456

38 Samples

Download data: TSV

(Submitter supplied) BACKGROUND: Glucocorticoid (GC) refractoriness is a common and unpredictable phenomenon in ulcerative colitis (UC). Although it has been demonstrated that NFkB is involved in its mechanism of action (MoA), there are no conclusive studies on the molecular functions involved. The current study describes in depth the MoA related to GC failure, by integrating transcriptomic data from UC patients, and updated molecular data on UC and GC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

38 Samples

Download data: TXT

(Submitter supplied) Background/aims: Changes in gene expression profiles among individuals with inflammatory bowel diseases (IBDs) could potentially influence the responsiveness to anti-TNF treatment. The aim of this study was to identify genes that could serve as predictors of early response to anti-TNF therapies in pediatric IBD patients prior to the initiation of treatment.Methods: We conducted a prospective, longitudinal, and multicenter study, enrolling 24 pediatric IBD patients aged less than 18 years who were initiating treatment with either infliximab or adalimumab. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

24 Samples

Download data: XLSX

(Submitter supplied) Background and Aims: Gene expression analysis of colon biopsies using high-density oligonucleotide microarray can contribute to the understanding of local pathophysiological alterations and to functional classification of precancerous adenoma, different stage colorectal carcinomas (CRC) and inflammatory bowel diseases (IBD). Results: Significant overexpression of collagen IV, lipocalin-2, caveolin-1, calumenin genes, and significant dowregulation of aquaporin-8, amnionless homolog, prostaglandin D2 receptor genes were detected in CRC patients compared to normal. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

53 Samples

Download data: CEL

(Submitter supplied) To elucidated through an unbiased manner which genes and pathways are differentially regulated during mouse colonic inflammation followed by a tissue regeneration phase. In particular, we took advantage of the widely used dextran sodium sulfate (DSS)-induced model of colitis. This model is one of the few characterized by a phase of damage followed by a phase of regeneration. Therefore, this model gave the possibility to identify also sets of genes essential in the regeneration phase, a key step towards the resolution of the inflammation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

26 Samples

Download data: CSV, TSV

(Submitter supplied) We used microarrays to identify markers predicting responder status in infliximab treatment in 19 rheumatoid arthritis and 20 Crohn's disease patients at week 0 and week 2 of treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

78 Samples

Download data: CEL, CHP