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 |