Chip enrichment analysis chea database

Author: fdjy

August undefined, 2024

WebJul 26, 2024 · Here, we describe TFEA.ChIP, an R package that exploits the vast amount of publicly available ChIP-seq datasets to perform TR enrichment analysis. Specifically, the internal database in TFEA.ChIP was built using the information in ReMap (Chèneby et al., 2024), as a source of uniformly processed ChIP-seq datasets and the evidences linking ... WebThe database contains 189 933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31 932 target genes. We used the database to analyze mRNA expression data where we perform gene-list enrichment analysis using the ChIP-X database as the prior biological knowledge gene-list library.

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Web1. The ChIP-x Enrichment Analysis (ChEA) database [10] is our own resource for storing putative targets for transcription factors extracted from publications that report experiments of profiling transcription factors binding to DNA in mammalian cells. The database is already formatted into a gene-set library where the WebMar 26, 2024 · GO and KEGG pathway enrichment analysis were performed to determine the biological functions of the DEGs (Wu et al. 2024). GO is commonly used to annotate genes from high-throughput genome or transcriptome data. ... ChIP enrichment analysis (ChEA) database was used. ChEA database provides data on eukaryotic transcription … significance of finding a bluebird feather

ChEA: transcription factor regulation inferred from …

WebThis data is often publicly available through several databases such as ChIP Enrichment Analysis (ChEA), hmChIP and ChIPbase (Chen et al., 2011;Lachmann et al., 2010; Yang et al., 2013). Over the ... WebMay 4, 2024 · To determine whether a particular transcription factor was the master regulator of the proteins more abundant in either sensitive or resistant cells, we performed a transcription factor enrichment analysis using the ChIP enrichment analysis (ChEA) database 25, 26 (Fig. 2b). N1 was found to be the most significantly enriched … WebThen we get a bar graph that displays, visualizes the enrichment level for each of those terms in the ChEA database. The ChEA database is a manually curated database that we develop in our lab, where we extract … significance of finding a white feather

Single-cell transcriptome reveals diversity of Müller cells with ...

GitHub - MaayanLab/ChEA: ChIP-X Enrichment Analysis

WebFu Y, Bi Z, Ji H, Elangbam M, Zhang Q, Qiu Y, Zhang W, Thakur C, Chen F. Disruption of the tumor suppressor-like activity of aryl hydrocarbon receptor by arsenic in epithelial cells and human lung cancer. WebOct 1, 2010 · The system is delivered as a web-based interactive application called ChIP Enrichment Analysis (ChEA). With ChEA, users can input lists of mammalian gene … significance of financial inclusion upscWebApr 15, 2013 · The ChIP-x Enrichment Analysis (ChEA) database is our own resource for storing putative targets for transcription factors extracted from publications that report experiments of profiling transcription factors binding to DNA in mammalian cells. The database is already formatted into a gene-set library where the functional terms are the ... significance of finding a black feather

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Chip enrichment analysis chea database

WebKEGG pathway enrichment analysis The KEGG pathway enrichment analysis was per-formed for both the up-regulated and down-regulated DEGs by DAVID. Total of 20 pathways were enriched for the DEGs (Table 1; Supplementary Table 1). Among them, the up-regulated DEGs were enriched in 12 pathways and the most significant one was cell WebOct 4, 2024 · ChIP-Atlas. An integrative, comprehensive database to explore public Epigenetic dataset, including ChIP-Seq, DNase-Seq, ATAC-Seq, and Bisulfite-Seq data: ChIP-Atlas covers almost all public data …

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WebOct 7, 2013 · The DE genes from the Agilent oligonucleotide array data were searched against online databases to obtain a list of TFs that regulate these genes. The ChIP-X … WebAug 13, 2010 · We used the database to analyze mRNA expression data where we perform gene-list enrichment analysis using the ChIP-X database as the prior biological …

WebOct 1, 2010 · The system is delivered as a web-based interactive application called ChIP Enrichment Analysis (ChEA). With ChEA, users can input lists of mammalian gene … WebMay 4, 2024 · b ChIP enrichment analysis (ChEA) performed through Enrichr of all proteins belonging to Cluster1 or Cluster 2. The combined score merges the result of a Fisher exact test and of Z-score in one value.

WebMay 29, 2013 · The effect of ~6000 drug perturbations using ~1300 different drugs on gene expression is recorded in the CMAP database. … WebENCODE_ChIP-seq: Primary: 552: 118: 1570.4: 392667: Enrichr_Queries: Primary: 1404: 1404: 297.7: 409279: GTEx_Coexpression: Primary: 1607: 1607: 300.0: 468672: … In the past, we have developed and published ChEA and ChEA2 which are …

WebAn integrative web-based and mobile gene-list enrichment analysis tool that includes 172 gene-set libraries, an alternative approach to rank enriched terms, and various …

WebJun 13, 2024 · The ChEA (ChIP Enrichment Analysis) database does this. Prediction using motifs. Another possibility is to look at binding motifs and see whether your gene list is enriched in those. These will, however, be inactive in a given tissue or cell type if the chromatin is packed or the methylation state of the promotor is unfavorable. significance of finding a featherWebJul 2, 2024 · ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. The ChEA3 … significance of finding dimesWebDec 22, 2024 · Multi-step upstream transcriptional regulator enrichment analysis. The possible transcription factors regulating the functional status of different subclusters of Müller cells were enriched by transcriptional regulator enrichment analysis (TREA) (Burda et al., 2024). Briefly, four resource databases, including ChIP enrichment analysis (ChEA ... the puckett team slidell lahttp://www.maayanlab.net/X2K/ significance of financial ratiosWebIn this new release of Enrichr we updated our ChIP-x Enrichment Analysis (ChEA) database with gene sets extracted from forty new studies. The previous version is now … significance of finger lengthWebMay 22, 2024 · The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq … the puck fairWebMar 16, 2024 · differentially expressed gene set with the ChIP Enrichment Analysis (ChEA) database of transcription factor gene targets (Lachmann et al., 2010). Of the 199 transcription factors included in ChEA, 149 exhibited twice as many induced target genes (FC ≥ 1.5) as repressed target genes (FC ≤ 1.5), significance of finding a dead bird