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Links tagged with 'chromatin immunoprecipitation'

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CEASTool Content

http://ceas.cbi.pku.edu.cn

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

NAR Web Server Issue 2006
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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CENTDISTTool Content

http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/

Expression > Gene Regulation

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

NAR Web Server Issue 2011
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tagsandrogen receptors binding sites chromatin immunoprecipitation dna sequence analysis humans male prostatic neoplasms transcription factors transcriptional regulatory elements tumor cell line

ChIP-ArrayTool Content

http://wanglab.hku.hk/ChIP-Array

Expression > Gene Regulation

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

NAR Web Server Issue 2011
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tagsanimals binding sites chromatin immunoprecipitation gene expression profiling high-throughput nucleotide sequencing humans mice oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

HHMDDatabase Content

http://bioinfo.hrbmu.edu.cn/hhmd

Protein > Databases

Human Histone Modification Database (HHMD) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD incorporates 43 location-specific histone modifications in human. HHMD can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown.

NAR Database Issue 2010
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tagsalgorithms chromatin chromatin immunoprecipitation computational biology dna methylation gene expression profiling genetic databases histones humans protein databases

JASPARDatabase Content

http://jaspar.cgb.ki.se

DNA > Databases
Expression > Databases

JASPAR is an open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. The database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family.

NAR Database Issue 2010
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tagsalgorithms animals chromatin immunoprecipitation computational biology fungal proteins genetic databases genome humans nucleic acid databases protein binding protein databases transcription factors

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

MPromDb update 2010Database Content

http://bioinformatics.wistar.upenn.edu/MPromDb/

DNA > Databases

MPromDb (Mammalian Promoter Database) is a curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. Also integrated is a GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations.

NAR Database Issue 2011
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tagsanimals chromatin immunoprecipitation dna sequence analysis genetic promoter regions humans mice nucleic acid databases rna polymerase ii systems integration

PAPTool Content

http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

NAR Web Server Issue 2007
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tagsalgorithms animals cell proliferation cholesterol chromatin immunoprecipitation computational biology conserved sequence gene expression profiling gene expression regulation genetic databases genetic models genetic promoter regions genetic transcription humans mice protein binding transcription factors

PRI-CATTool Content

http://www.ab.wur.nl/pricat

Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

NAR Web Server Issue 2011
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tagsarabidopsis binding sites ChIP-seq chromatin immunoprecipitation dna-binding proteins genetic promoter regions high-throughput nucleotide sequencing plant proteins plants transcription factors

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals automated pattern recognition automation base sequence bayes theorem binding sites chromatin immunoprecipitation cluster analysis computational biology conserved sequence dna dna sequence analysis gene expression profiling humans mice molecular sequence data protein binding saccharomyces cerevisiae sequence alignment transcription factors