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Links tagged with 'chromatin'

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BIOBASE Gene Regulation databasesDatabase Content

http://www.gene-regulation.com/pub/databases.html

Protein > Interactions, Pathways, Enzymes

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

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tagsanimals binding sites chromatin chromosomes database management systems developmental gene expression regulation dna-binding proteins eukaryotic cells forecasting gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans macromolecular substances mice nuclear matrix nuclear proteins nucleic acid databases oligonucleotide array sequence analysis protein databases saccharomyces signal transduction systems integration tissue distribution transcription factors

DAnCERDatabase Content

http://wodaklab.org/dancer/

DNA > Databases

The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks.

NAR Database Issue 2011
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tagsanimals caenorhabditis elegans chromatin disease drosophila melanogaster epigenomics genetic databases humans mice molecular sequence annotation protein conformation protein interaction mapping saccharomyces cerevisiae

ExpressYourselfTool Content

http://array.mbb.yale.edu/analysis/

Expression > Transcript Expression Analysis

ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.

NAR Web Server Issue 2003
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tagsalgorithms chromatin gene expression profiling genomics oligonucleotide array sequence analysis precipitin tests

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

ICM WebTool Content

http://dna.ccs.tulane.edu/icm

DNA > Structure and Sequence Feature Detection

The Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.

NAR Web Server Issue 2010
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tagschromatin chromatin assembly and disassembly dna genetic promoter regions mouse mammary tumor virus nucleic acid conformation nucleosomes

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

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

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

NAR Web Server Issue 2004
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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

NCBI EpigenomicsDatabase Content

http://www.ncbi.nlm.nih.gov/epigenomics

DNA > Databases

The Epigenomics database is a resource for whole-genome epigenetic data sets. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes.

NAR Database Issue 2011
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tagschromatin epigenomics genetic databases humans
setsNational Center for Biotechnology Information (NCBI)