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Protocols

iTAK specifications

Information


Unique identifier OMICS_08093
Name iTAK
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 15.03
Stability Beta
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_08093
Name iTAK
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Version 15.03
Stability Beta
Maintained Yes

Publication for iTAK

iTAK citations

 (32)
library_books

Comparative transcriptomic analysis identifies genes responsible for fruit count and oil yield in the oil tea plant Camellia chekiangoleosa

2018
Sci Rep
PMCID: 5923238
PMID: 29703942
DOI: 10.1038/s41598-018-24073-z

[…] s conducted against Arabidopsis using KOBAS (version 3.0). Transcription factor and regulator analysis were conducted by using the DEG sequences as input against transcription factors in the database iTAK (http://itak.feilab.net/cgi-bin/itak/index.cgi, version 17.09) based on information from 169 plant genomes. […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] Transcription factors and protein kinases were identified using iTAK v1.5 (http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi). Carbohydrate-active enzymes (CAZymes) were identified by scanning using HMMER 3.0 against the Hidden Markov Model (HMMs) correspondin […]

library_books

Ginseng Genome Database: an open access platform for genomics of Panax ginseng

2018
BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] Transcription factors (TFs) are the key regulators for development and stimulus responses. TFs were identified based on the criteria of PlnTFDB [] using iTAK (http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi). A total of 4439 TF and transcription regulator genes were identified and classified into 94 TF families (http://ginsengdb.snu.ac.kr/tf_cla […]

library_books

Analysis of Transcriptional Responses of the Inflorescence Meristems in Jatropha curcas Following Gibberellin Treatment

2018
Int J Mol Sci
PMCID: 5855654
PMID: 29389867
DOI: 10.3390/ijms19020432

[…] hways, respectively [,]. Corrected p-value of 0.05 was set as the threshold for the significantly enrichment of GO terms and KEGG pathways. Transcription factor prediction analysis was carried out by iTAK v1.5 software (http://itak.feilab.net/cgi-bin/itak/index.cgi, 13 August 2012) []. The Blastx alignment was conducted between the DEGs and TAIR10 protein database (https://www.arabidopsis.org/). T […]

library_books

Transcriptome analysis of filling stage seeds among three buckwheat species with emphasis on rutin accumulation

2017
PLoS One
PMCID: 5738128
PMID: 29261741
DOI: 10.1371/journal.pone.0189672

[…] We used iTAK software to analyze the transcription factors in Fes, Fea and Ft buckwheat species []. We identified 2379 unigenes as transcription factors. The main transcription factor families identified were […]

library_books

Comprehensive Genome Wide Classification Reveals That Many Plant Specific Transcription Factors Evolved in Streptophyte Algae

2017
Genome Biol Evol
PMCID: 5737466
PMID: 29216360
DOI: 10.1093/gbe/evx258

[…] nd subfamilies (, ; 81 of them TFs) our rule set is the most comprehensive one for plant TAPs, since other approaches have significantly less resolution, for example, 58 in PlantTFDB 4.0 () and 72 in iTAK (). We compared the TAPscan v1 and v2 annotations with a number of A. thaliana and P. patens phylogeny-based family classifications defined as gold standard (; ; ; ). We find that the average sen […]


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