Bioinformatics Resources for Microarray data analysis, Protein function/structure prediction, and Protein-protein interaction databases

Supplemental Materials for the paper "Bioinformatics resources for cancer research with an emphasis on protein function and structure prediction tools" by Daisuke Kihara, Yifeng David Yang and Troy Hawkins, Cancer Informatics, 2:25-35, (2006).



Microarray Analysis Software
Microarray Data Repositories
Protein Function Prediction Tools
Protein Structure Prediction Tools
Additional Structure Prediction Tools
Protein Protein Interaction Databases & Database Tools
Other bioinformatics links




Microarray Analysis Software

Software Location Web Site
GoMiner NCI, NIH http://discover.nci.nih.gov/gominer/
GoSurfer Harvard Univ. http://www.biostat.harvard.edu/complab/gosurfer/
GenMAPP UC San Francisco http://www.genmapp.org
ArrayTrack US Food and Drug Administration (FDA) http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm
caGEDA Univ. of Pittsburgh http://bioinformatics.upmc.edu/GE2/GEDA.html
SAM Stanford Univ. http://www-stat.stanford.edu/~tibs/SAM/
NUDGE Univ. of Washington http://www.bioconductor.org

 

Microarray Data Repositories

Software Location Web Site
GEO NCBI, NIH http://www.ncbi.nlm.nih.gov/projects/geo/
ArrayExpress EMBL-EBI http://www.ebi.ac.uk/arrayexpress/
CIBEX Nat. Inst. Genetics, Japan http://cibex.nig.ac.jp
Standard Microarray Database (SMD) Stanford Univ. http://smd.stanford.edu/

The Gene Expression Database (GXD) The Jackson Lab. http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml
Oncomine Univ. of Michigan http://www.oncomine.org

 

Protein Function Prediction Tools

Software Type Location Web Site
BLAST Homology search NCBI, NIH http://www.ncbi.nlm.nih.gov/BLAST

select protein-protein BLAST
FASTA Homology search Virginia Univ.

Kyoto Univ.
http://fasta.bioch.virginia.edu

http://fasta.genome.jp/
PSI-BLAST Homology search NCBI, NIH http://www.ncbi.nlm.nih.gov/BLAST

select PSI- and PHI-BLAST
Pfam Protein family identification Washington Univ. http://pfam.wustl.edu
SMART Conserved Motif search EMBL http://smart.embl-heidelberg.de
PROSITE Functional Motif search Swiss Inst. Bioinformatics http://us.expasy.org/prosite

http://motif.genome.ad.jp
ELM Functional motif search in eukaryotes The ELM Consortium http://elm.eu.org
STRING Function prediction by comparative genomics EMBL http://string.embl.de
PSORT Subcellular localization prediction Human Genome Center, Tokyo Univ. http://www.psort.org
PFP Function prediction by mining  PSI-BLAST result Purdue Univ. http://dragon.bio.purdue.edu/pfp

 

Protein Structure Prediction Tools

Software Type Location Web Site
PSIPRED 2ndary structure Univ. College London http://bioinf.cs.ucl.ac.uk/psipred/
PORTER 2ndary structure Univ. College Dublin http://distill.ucd.ie/porter/
SAM-T02 2ndary structure UC Santa Cruz http://www.cse.ucsc.edu/research/compbio/HMM-apps/T02-query.html
SABLE 2ndary str., solvent accesibility Cincinnati Children's Hospital Med. Center http://sable.cchmc.org/
PredictProtein 2ndary structure and others Columbia Univ. http://cubic.bioc.columbia.edu/predictprotein/
COILS Coiled-coil region EMBnet, Switzerland http://www.ch.embnet.org/software/COILS_form.html
GlobPlot Disordered region EMBL http://globplot.embl.de/
PONDR Disordered region Indiana Univ. http://www.pondr.com/
TMHMM Transmembrane domain Technical Univ. of Denmark http://www.cbs.dtu.dk/services/TMHMM-2.0/
HMMTOP Transmembrane domain Hungarian Academy of Sciences http://www.enzim.hu/hmmtop/

SWISS-MODEL 3D structure; (Homology modeling) Swiss Inst. of Bioinformatics http://swissmodel.expasy.org

HHPred 3D str.; (Homology modeling) Max-Planck Inst. http://protevo.eb.tuebingen.mpg.de/toolkit/index.php?view=hhpred

MODELLER 3D str.; (Homology modeling) UC San Francisco http://salilab.org/modeller/

FUGUE 3D str., threading Univ. of Cambridge http://www-cryst.bioc.cam.ac.uk/~fugue/

Phyre 3D str., threading Imperial College London http://www.sbg.bio.ic.ac.uk/~phyre/

SPARKS 3D str., threading SUNY Buffalo http://phyyz4.med.buffalo.edu/hzhou/anonymous-fold-sparks2.html
Robetta 3D str; ab initio Univ. Washington http://robetta.bakerlab.org/

 

Additional Structure Prediction Tools

Tool/DB Type Location Website
GOR IV 2ndary structure PBIL,Lyon, France http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html
PROF 2ndary structure University of Wales, Aberystwyth http://www.aber.ac.uk/%7Ephiwww/prof/
PSA 2ndary structure & 3D str., threading Boston University http://bmerc-www.bu.edu/psa/#topics
Protinfo protein 3D/2D str. and others University of Washington, Seattle

http://protinfo.compbio.washington.edu/

3D-JIGSAW 3D str.; (Homology modeling) Cancer Research UK London Research Institute http://www.bmm.icnet.uk/servers/3djigsaw/
ESyPred3D 3D str.; (Homology modeling) The University of Namur, Belgium. http://www.fundp.ac.be/urbm/bioinfo/esypred/
GENO3D 3D str.; (Homology modeling) PBIL,Lyon, France http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html
DSC1 3D str.; (Homology modeling) San Diego Supercomputer Center (SDSC). http://cl.sdsc.edu/hm.html
FoldClass 3D str., threading DKFZ,Heidelberg, Germany http://genome.dkfz-heidelberg.de/cgi-bin/w2hdemo/nph-w2h.helpapp?foldclass
Fold Recognition 3D str., threading UCLA http://www.doe-mbi.ucla.edu/Services/FOLD/

 

Protein Protein Interaction Databases & Database Tools

DB/Software Type Location Web Site
BIND PPI, pathway Mt. Sinai Hospital, Canada http://bind.ca/

DIP PPI UC Los Angeles http://dip.doe-mbi.ucla.edu/
MIPS Mammalian PPIs Munich Information Center for Protein Sequences http://mips.gsf.de/proj/ppi/

HPRD Human protein references Johns Hopkins Univ. http://www.hprd.org/

GRID genetic and physical interactions of yeast, fry, worm Mt. Sinai Hospital, Canada http://biodata.mshri.on.ca/grid/

IntAct open source db systems & tools for PPI data EBI http://www.ebi.ac.uk/intact/

Ospray PPI visualization tool Mt. Sinai Hospital, Canada http://biodata.mshri.on.ca/osprey/

 

Other bioinformatics links

Tool/DB Type Location Website
Structure Prediction & Databases Resources San Diego Supercomputer Center (SDSC). http://restools.sdsc.edu/biotools/biotools9.html
NIH Molecular Modeling Homepage Resources NIH,USA http://cmm.info.nih.gov/modeling/
Microarray Software Comparison Links The Chinese Univ. of Hong Kong, China http://ihome.cuhk.edu.hk/~b400559/arraysoft_rpackages.html

 


Maintained by Yifeng D. Yang, questions and comments to yang41@ purdue.edu
Last updated on Jan 6 2006.