Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-GEOD-100100

ABSTRACT: A data mining paradigm for identifying key factors in biological processes using gene expression data

PROVIDER: E-GEOD-100100 | ExpressionAtlas | 2020-04-01

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-GEOD-100100-analysis-methods.tsv	Tabular
	E-GEOD-100100-analytics.tsv	Tabular
	E-GEOD-100100-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-100100-configuration.xml	Xml
	E-GEOD-100100-g2_g1-mvaPlot.png	Other

Items per page:

1 - 5 of 20

Similar Datasets

Mus musculus

Project description:A data mining paradigm for identifying key factors in biological processes using gene expression data

| PRJNA390718 | ENA

Biomarks of Resistance to Cetuximab in Colorectal Cancer

Project description:Interventions: A group:Before using cetuximab;B group:After progression of disease:no Primary outcome(s): KRAS gene sequence;NRAS gene sequence;BRAF gene sequence;PIK3CA gene sequence;EGFR gene sequence;EGFR gene copy numbers;EGFR expression;Her2 expression;c-Met expression;PTEN expression Study Design: historical control

| 2671639 | ecrin-mdr-crc

Modeling transcriptional cis-regulation with a library of genome-wide histone H3K27ac profiles

Project description:We describe, MARGE, Model-based Analysis of the Regulation of Gene Expression, a robust methodology that leverages a large library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. MARGE adopts a gene centric approach to define a regulatory potential that summarizes the aggregate activity of multiple cis-regulatory elements on each gene. This model is effective in describing cis-regulatory activity and, unlike the super-enhancer based approach, is highly predictive of gene expression changes in response to BET-bromodomain inhibitors. We show that linear combinations of H3K27ac defined regulatory potentials, selected from an extensive database of published H3K27ac profiles, can accurately model diverse gene sets derived from differential gene expression experiments. In addition, we demonstrate a novel semi-supervised learning approach for identifying transcription factor binding sites associated with the set of transcription factors that regulate the gene set. MARGE leverages published H3K27ac ChIP-seq data to enhance the interpretation of newly generated H3K27ac ChIP-seq profiles. MARGE can also be used to analyze gene expression studies, without the production of matched H3K27ac ChIP-seq data. Identifying genomic profiles of histone modification H3K27ac in LNCaP-abl cell line after siRNA knock down of a series of gene factors.

2016-05-16 | E-GEOD-72467 | biostudies-arrayexpress

Fuzheng Yiliu-1010

Project description:Real world study was used to evaluate the therapeutic effect of Fuzheng anti-tumor therapy on colorectal cancer patients in stage II and III after surgery and standard chemotherapy, and the prediction model of dominant population of Fuzheng anti-tumor therapy was constructed by using real-world data and gene expression profile data.

| 2344714 | ecrin-mdr-crc

Analysis of factors bound to native metaphase ESC chromosomes following purification by flow cytometry

Project description:Stem cells are able to self-renew and also generate differentiated progeny. How gene expression patterns are transmitted through mitosis remains unresolved. Conventional studies have relied upon rigorous cell-cycle-stage synchronisation to find factors in mitotic lysates that could ‘bookmark’ the genome. Here we use an alternative approach, purifying native-unfixed mitotic chromosomes from different cell types using flow cytometry and directly identifying chromosome-bound proteins by LC-MS/MS. This revealed a rich profile of pluripotency- and lineage-specific transcription factors that remained bound to mitotic chromosomes in pluripotent ESCs and lymphocytes, as well as factors implicated in chromosome condensation, architecture and gene silencing. Removal of DNA methylation, PRC2 activity, or in situ cleavage of cohesin, each resulted in the reduced compaction of mitotic chromosomes. These data provide a comprehensive catalogue of bookmarking factors in pluripotent versus lineage-restricted cells and demonstrate an expected duality of function by candidates in regulating both gene expression and mitotic chromosome structure.

2020-06-15 | PXD015251 | Pride

Comparative transcriptome analysis of Th22 and Th17 cells

Project description:Microarray was used to delineate the global gene expression profile underlying the specific developmental program of two divergent antigen-specific T helper subsets (Th22 versus Th17) by identifying upregulation or downregulation of key lineage-determining transcription factors, cytokines, chemokines and other genes that govern their functional attributes.

2013-01-29 | GSE42332 | GEO

Genome-wide mapping of histone methylation in human melanocytes and melanoma cell lines

Project description:Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression during melanomagenesis.

2013-12-01 | GSE33930 | GEO

Corral2021 - Interplay between SMAD2 and STAT5A regulating IL-17A/F expression in Th cells.

Project description:IL-17A and F are critical cytokines in anti-microbial immunity but also contribute to auto-immune pathologies. Recent evidence suggests that they may be differentially produced by T-helper (Th) cells but the underlying mechanisms remain unknown. To address this question, a logical model containing 82 components and 136 regulatory links was developed and calibrated with original flow cytometry data using naive CD4+ T cells in conditions inducing either IL-17A or F. Model analyses led to the identification of the transcription factors NFAT2A, STAT5A and Smad2 as key components explaining the differential expression of IL-17A and IL-17F, with STAT5A controlling IL-17F expression, and an interplay of NFAT2A, STAT5A and Smad2 controlling IL-17A expression.

2021-04-06 | MODEL2101150001 | BioModels

Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors

Project description:Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors

| PRJNA561759 | ENA

Genome-wide mapping of histone methylation in human melanocytes and melanoma cell lines

2013-12-01 | E-GEOD-33930 | biostudies-arrayexpress