Home  |  About Startbioinfo  |  Other web-portals | BdataA  | 

  
Table: A comparative account of tools for transcript expression prediction using existing transcriptomics data
Features TIPMaP BEAT GATExplorer SpliceAV Alexa-Seq C-It MMBGX FIRMAGene ASAP II Brainarray AceView EDAS fastDB Splice & Neihborhood TissueInfo
PMID NA 22536968 20429936 20184770 20835245 20628071 19854940 19463149 17108355 17586830 16925834 16909834 16052034 11435406 11691939
Date of publication NA 2012 2010 2010 2010 2010 2010 2009 2007 2007 2006 2006 2005 2001 2001
Working status Y Y Y Codes available on request Y Y Codes are available at the link provided (But the link is not active) Codes available on request Y Y Y Y Y Codes available on request Y
Web based application Y Y Y Codes available on request Y Y Codes are available at the link provided (But the link is not active) Codes available on request Y Y Y Y Y Codes available on request Y
Species Human, mouse, rat Human Human, mouse & rat Any Human & mouse Human, mouse, rat, chicken & zebrafish Human, mouse & rat Human 15 12, including human Human, mouse, rat, C.elegans, A.thaliana Human, mouse, dog & rat Human Rat Human & mouse
Reannotation of probe sequences Y NA Y (only for display purpose) NA NA NA Y N (used the annotations as provided by Affymetrix) NA Y NA NA NA EST NA
Probe sequences are alingned to Refseq transcripts NA ENSEMBL NA NA NA Ensembl N (used the annotations as provided by Affymetrix) NA Ensembl, Vega (gene, transcript, exon), entrez, RefSeq, Unigene NA NA NA NA NA
Types of probes chosen Probes specific to a transcript NA NA NA NA NA Probes specific to a transcript N (used the annotations as provided by Affymetrix) NA Probes specific to a transcript as well as probes common to transcript isoforms NA NA NA NA NA
Source for expression information Affymetirx microarray (31 platforms for human) Affymetrix exon arrays Affymetrix (HG_U133A) Affymetirx microarray platforms RNA seq data Affymetrix HGU133A and exon array Affymetrix exon arrays Affymetrix Gene 1.0 ST platform EST Affymetirx microarray (14 platforms for human) EST EST EST & cdna Affymetrix EST
Identification of transcript's expression (Detected) Y N NA Displays the probe-sets, which are differentially regulated. The data has to be re-analyzed, to identify the transcript level expression N N N NA N Additional softwares required Y N Y N Y
Identification of transcript's expression (Differentially regulated) Y N NA Displays the probe-sets, which are differentially regulated. The data has to be re-analyzed, to identify the transcript level expression. Y N Y NA N Additional softwares required N N N Y N
Process the gene expression data Y N NA N NA NA NA NA NA Y NA NA NA NA NA
Analysis/Filtering Y N NA Y NA NA NA NA NA N NA NA NA NA NA
Gene based search Y Y Y NA Y Y NA NA Y N Y Y Y NA N
Transcript based search Y N N NA N N NA NA Y N N Y N NA Y
Keyword (testis, expression, brian) search Y Y Y NA Y Y NA NA Y Y N Y Y NA Y (tissue search)
Search by GEO ID's Y NA NA NA NA NA NA NA NA Y NA NA NA NA NA
Displays gene information Y Y Y NA Y Y NA NA Y N Y N Y NA N
Dispalys protein information Y N N NA N N NA NA N N Y N Y NA N
Displays transcript information Y Y Y NA Y Y NA NA Y N Y N Y NA N
Displays BLAST alignment results Y N Y NA NA NA NA NA NA N NA NA NA NA NA
Displays transcript specific probe-sets Y N Y NA NA NA NA NA NA N NA NA NA NA NA
Download analysis results Y N N NA NA NA NA NA NA N NA NA NA NA NA
Dowload custom CDF Y N Y NA NA NA NA NA NA Y NA NA NA NA NA
Dowload R and perl programs Y N Y NA NA NA NA NA NA Y NA NA NA NA NA
Comments Can perform structural and sequence analysis. Can be used to find splicing regulatory motifs. Can download gene, exon and intron sequences in FASTA format Exon array data can be uploaded and analyzed. Otherwise the data quantum is very less. Gives the exons, which are differentially regulated, which have to be extrapolated to identify the differentially regulated splice forms. Gives expression at gene level, using expression data from GSE1133. Limited to a few normal tissues. For every tissue, expression per probe is displayed in a bar graph. A gene should have more than one probe-set, and the probe-set, which have a different expression pattern than the others is picked, and then it is used to predict the possible alternative mRNA processing. Limited to 13 RNA sequence libraries Gives expression at gene level, for a few normal tissues. Also, displays differentially regulated exons based on Exon array data. Probes are grouped based on the annotations provided by Affymetrix and are used to identify the genes which undergo differential splicing. Limited to a few normal tissues Limited to a few normal tissues Gives expression at gene level, for a few normal tissues Limited to 36 normal tissues. Displays the number of transcript isoforms detected in each tissue Expression is determine at probe-level to predict the differntially expressed splice variants using Splice and Neighborhood algorithms. The data can be viewed using Spotfire program. To identify the candidate transcripts,EST database is searched using the Compugen LEADS program Limited to a few normal tissues
  

copyright © Dr. Kshitish Acharya K; all rights reserved