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Protocols

TFSearch specifications

Information


Unique identifier OMICS_29534
Name TFSearch
Interface Web user interface
Restrictions to use None
Input data A DNA sequence.
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

TFSearch citations

 (176)
library_books

STAT3 activated CD36 facilitates fatty acid uptake in chronic lymphocytic leukemia cells

2018
Oncotarget
PMCID: 5940394
PMID: 29765537
DOI: 10.18632/oncotarget.25066

[…] Because STAT3 is constitutively activated in CLL cells [], we wondered whether overexpression of CD36 is driven by STAT3. Using the TFSEARCH database [] we identified 4 GAS-like elements, known as putative STAT3-binding sites [], within 600 bp upstream of the CD36 gene start codon (Figure ). To determine whether STAT3 binds to any […]

library_books

Aberrant expression and DNA methylation of lipid metabolism genes in PCOS: a new insight into its pathogenesis

2018
Clin Epigenetics
PMCID: 5767000
PMID: 29344314
DOI: 10.1186/s13148-018-0442-y

[…] s. However, the correlation was compromised in PCOS women, especially for BNIP3. As for LIF, there was only one differentially methylated CpG site; however, the prediction of transcription factors by TFSEARCH (http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/TFSEARCH.html) and DBD: Transcription factor prediction database (http://www.transcriptionfactor.org/index.cgi) revealed that the d […]

library_books

Fibronectin is a stress responsive gene regulated by HSF1 in response to geldanamycin

2017
Sci Rep
PMCID: 5732156
PMID: 29247221
DOI: 10.1038/s41598-017-18061-y

[…] inin beta 3 [LAMB3], laminin gamma 2 [LAMC2], collagen 4 alpha 2 [COL4A2], collagen 4 alpha 3 [COL4A3], elastin [ELN], vitronectin [VTN] and osteopontin [SPP1]) were screened for potential HSEs using TFSearch. The locations of predicted HSEs on the gene promoter regions are shown as black boxes (Fig. ). At least one putative HSE was predicted in the promoter regions of all the genes analysed (Fig. […]

call_split

IL 2 imprints human naive B cell fate towards plasma cell through ERK/ELK1 mediated BACH2 repression

2017
Nat Commun
PMCID: 5682283
PMID: 29129929
DOI: 10.1038/s41467-017-01475-7
call_split See protocol

[…] MatInspector, TFBIND, TFSEARCH (http://cbrc3.cbrc.jp/papia/howtouse/howtouse_tfsearch.html), PROMO and comparative genomics tool rVISTA were used for the identification of regulatory elements in human BACH2 locus. BLAST pr […]

library_books

E2F1 silencing inhibits migration and invasion of osteosarcoma cells via regulating DDR1 expression

2017
PMCID: 5673022
PMID: 29039472
DOI: 10.3892/ijo.2017.4165

[…] oreover, the truncated DDR1 promoter without the region (−200/−50) failed to respond to E2F1 knockdown (). Then, we analyzed the promoter sequence around −200 bp by bioinformatic software (JASPAR and Tfsearch), and a putative E2F1 binding site (AATGCCGC) was identified (). Furthermore, mutation of the site greatly diminished the inhibitory effect of E2F1 silence on the transcription activity of DD […]

library_books

A functional IL1RL1 variant regulates corticosteroid induced sST2 expression in ulcerative colitis

2017
Sci Rep
PMCID: 5579262
PMID: 28860510
DOI: 10.1038/s41598-017-10465-0

[…] and proximal promoters was performed using published human IL1RL1 sequences from the GenBank™/ EMBL database (accession No. AC007248). The transcription factor binding site search was performed using TFsearch version 1.3 (Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan), MatInspector (Genomatrix Software, Munchen, Germany), TF […]

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TFSearch institution(s)
Computational Biology Research Center , AIST, Tokyo, Japan

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