PAZAR Documentation

Links

Content

Useful software

Introduction

The data found within PAZAR can be used in association with a large array of online resources. We do not directly provide such tools within PAZAR. We believe the data should be accessed by sequence analysis tools through the PAZAR software interface. For now, one must still copy data from PAZAR and paste it into the web services you choose to use. The following list of resources is not comprehensive. If you have encountered a program that you think is noteworthy, please let us know.

Software Classes

Class Description
"TFBS Discrimination" Given a count matrix summarizing the binding sites for a TF, predict TFBS in a sequence of your choice.
"Pattern Discovery" Given a set of regulatory sequences, you wish to find new patterns that might be a novel type of TFBS.
"TFBS Over-representation" Given a set of genes and a count matrix, you wish to determine if the pattern defined by the count matrix is significantly enriched compared to background. Unfortunately there is no TFBS over-representation tool that allows for user-submitted binding profiles. Tools like oPOSSUM must analyze enormous numbers of genes to perform the analysis and therefore do not offer submission (yet).
"TFBS Model Comparison" You have recovered a new TFBS pattern (count matrix) and wish to see if the pattern resembles other known TFBS profiles. Once you find a pattern, it is natural to want to compare it against a database of patterns to see if it matches a characterized type of TFBS.
"TFBS Combination Detection" You have a set of TFBS count matrices (1 or more), and wish to find segments in a DNA sequence significantly enriched for combinations of matches to the pattern(s).
"TF Information" Sometimes you need to look up information about a gene or protein. Everyone knows about Enrez Gene and UniProt. You might also try http://www.transcriptionfactors.org/.

Software list

Name Classes URL
AHAB TFBS Combination Detection http://gaspard.bio.nyu.edu/Ahab.html
Cluster Buster TFBS Combination Detection http://zlab.bu.edu/cluster-buster/cbust.html
ConSite TFBS Discrimination http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/
CRE works TFBS Discrimination
TFBS Combination Detection
http://genereg.ornl.gov/scancre/
FOOTER TFBS Discrimination http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php
JASPAR TFBS Model Comparison http://jaspar.genereg.net/
MAST TFBS Discrimination
TFBS Combination Detection
http://meme.sdsc.edu/meme/mast.html
MSCAN TFBS Combination Detection
RSA TOOLS TFBS Discrimination
Pattern Discovery
http://rsat.ulb.ac.be/rsat/
STAMP TFBS Model Comparison http://www.benoslab.pitt.edu/stamp/
TOUCAN TFBS Discrimination
Pattern Discovery
TFBS Combination Detection
http://homes.esat.kuleuven.be/~saerts/software/toucan.php
WebMotifs Pattern Discovery http://fraenkel.mit.edu/webmotifs/

Regulatory datasets

Name Description and URL
ABS A database of annotated regulatory binding sites from orthologous promoters. http://genome.imim.es/datasets/abs2005/downloads.html
AGRIS AtcisDB and AtTFDB An Arabidopsis thaliana cis-regulatory and transcription factor database. http://arabidopsis.med.ohio-state.edu/
AtProbe An Arabidopsis thaliana promoter binding element database. http://rulai.cshl.edu/cgi-bin/atprobe/atprobe.pl
AthaMap A genome-wide map of potential transcription factor binding sites in Arabidopsis thaliana. http://www.athamap.de/
BOND The biomolecular object network databank (BOND) is a resource to perform cross-database searches of available sequence, interaction, complex and pathway information. http://bond.unleashedinformatics.com/Action?
CEPDB A Caenorhabditis elegans promoter database. http://rulai.cshl.edu/cgi-bin/CEPDB/home.cgi
Cisreg.ca Our laboratory website that features a muscle and liver data set. http://www.cisreg.ca/tjkwon/
Compel Composite regulatory elements—structure, function and classification. http://compel.bionet.nsc.ru/new/compel/compel.html
DATF The Database of Arabidopsis thaliana transcription factors (DATF). http://datf.cbi.pku.edu.cn/
DBTSS A database of transcriptional start sites (TSS). http://dbtss.hgc.jp/
DoOP An orthologous-clusters-of-promoters database. http://doop.abc.hu/
DBSD A drosophila binding site database. Please note that this website is not yet functional but will be soon. http://rulai.cshl.org/dbsd/index.html
Drosophila DNase I Footprint Database A webpage providing access to results of the systematic curation and genome annotation of 1,365 DNase I footprints for the fruitfly Drosophila melanogaster. http://www.flyreg.org/
DRTF A database of rice transcription factors. http://drtf.cbi.pku.edu.cn/
ECRBase A database of evolutionary conserved regions (ECRs), promoters, and transcription factor binding sites in vertebrate genomes created using ECR browser alignments. http://ecrbase.dcode.org/
EDGEdb PDI, PPI and gene expression data generated by the Walhout laboratory and others are made available to the community through EDGEdb (elegans differential gene expression data). http://edgedb.umassmed.edu/IndexAction.do
EPD A eukaryotic promoter database. http://www.epd.isb-sib.ch/
ERTargetDB ERTargetDB integrates information from ongoing chip-on-chip experiments and promoter sequence conservation from the OMGProm database. http://bioinformatics.med.ohio-state.edu/ERTargetDB/
Globin Gene Server A database for experimental data on the regulation of the globin gene cluster. http://globin.cse.psu.edu/
Harbison Lab Datasets useful in comparative genomics and in erythroid gene regulation. http://www.bx.psu.edu/~ross/dataset/DatasetHome.html
HemoPDB A hematopoiesis promoter database. http://bioinformatics.med.ohio-state.edu/HemoPDB/
JASPAR A high-quality transcription factor binding profile database. http://jaspar.genereg.net
LSPD The liver specific gene promoter database. http://rulai.cshl.edu/LSPD/
MPD A mammalian promoter database for human, mouse and rat. http://rulai.cshl.edu/CSHLmpd2
MPromDb A mammalian promoter database with experimentally supported annotations.
http://bioinformatics.med.ohio-state.edu/MPromDb/
MTIR A database for muscle-specific regulation of transcription. http://www.cbil.upenn.edu/MTIR/HomePage.html
OMGProm A database for orthologous mammalian gene promoters. http://bioinformatics.med.ohio-state.edu/OMGProm/
ooTFD An object-oriented transcription factors database. ttp://www.ifti.org/ootfd/
OPD An osteo-promoter database—promoters of genes in the osteogenic pathway. http://www.opd.tau.ac.il/
Oreganno Open regulatory annotation database. http://oreganno.org
PLACE A database of plant cis-acting regulatory DNA elements. http://www.dna.affrc.go.jp/PLACE/
Plant CARE A cis-acting regulatory element database for plants. http://intra.psb.ugent.be:8080/PlantCARE/
Plant Prom DB A database of plant promoter sequences. http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
RARTF The RIKEN arabidopsis transcription factor database. http://rarge.gsc.riken.jp/rartf/
REDfly Regulatory element database for drosophila. http://redfly.ccr.buffalo.edu/?content=/search.php
RiceTFDB Rice genes involved in transcriptional control. http://ricetfdb.bio.uni-potsdam.de/v2.1/
RIKEN TFdb A mouse transcription factor database. http://genome.gsc.riken.jp/TFdb/
rSNP Influence of single nucleotide mutations in regulatory gene regions. http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
SCPD A Saccharomyces cerevisiae promoter database. http://rulai.cshl.edu/SCPD/
Stanford Encode Project An encyclopedia of DNA elements. http://www-shgc.stanford.edu/genetics/encode.html
Transcription Factors DD A database for transcription factors of humans and other organisms. http://www.proteinlounge.com/trans_home.asp
TRANSFAC A database for eukaryotic transcription factors and their binding profiles. http://www.gene-regulation.de/
TRED The transcriptional regulatory element database. http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
TRRD A database for transcription regulatory regions. http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/
VISTA Enhancer Browser A database of tissue-specific human enhancers. http://enhancer.lbl.gov