> Tag > Links tagged with 'chromatin immunoprecipitation'

Links tagged with 'chromatin immunoprecipitation'

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CEASTool Content

http://ceas.cbi.pku.edu.cn [open in a new window]

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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.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
CEAS: cis-regulatory element annotation system200673
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/ [open in a new window]

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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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
CENTDIST: discovery of co-associated factors by motif distribution20116
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 [open in a new window]

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor20113
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 [open in a new window]

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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.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
HHMD: the human histone modification database201016
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 [open in a new window]

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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.

links directory index: 119
TitlePublication YearGoogle Scholar Citation Count
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles2010119
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/ [open in a new window]

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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).

links directory index: 90
TitlePublication YearGoogle Scholar Citation Count
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data20075
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension200485
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/ [open in a new window]

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data20113
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 [open in a new window]

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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.

links directory index: 72
TitlePublication YearGoogle Scholar Citation Count
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis200719
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles200653
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

PeakSeqTool Content

http://archive.gersteinlab.org/proj/PeakSeq/ [open in a new window]

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DNA > Mapping and Assembly
Expression > Gene Regulation
Expression > Transcript Expression Analysis

PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

links directory index: 216
TitlePublication YearGoogle Scholar Citation Count
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls2009216
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tagsbinding sites biotechnology chromatin chromatin immunoprecipitation dna dna sequence analysis false positive reactions genetic models genetic variation genome genomics humans oligonucleotide array sequence analysis rna polymerase ii

PRI-CATTool Content

http://www.ab.wur.nl/pricat [open in a new window]

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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.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments20115
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

SISSRsTool Content

http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/ [open in a new window]

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DNA > Mapping and Assembly
Expression > Gene Regulation
Expression > Transcript Expression Analysis

SISSRs (Site Identification from Short Sequence Reads), an algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

links directory index: 233
TitlePublication YearGoogle Scholar Citation Count
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data2008233
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tagsalgorithms base sequence binding sites chromatin immunoprecipitation dna-binding proteins genomics hela cells humans jurkat cells molecular sequence data repressor proteins stat1 transcription factor transcription factors transcriptional regulatory elements

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/ [open in a new window]

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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.

links directory index: 80
TitlePublication YearGoogle Scholar Citation Count
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches200729
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data200651
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

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