Cistrome – Platform for Transcriptional Regulation Studies

Cistrome

:: DESCRIPTION

Cistrome is a web-based integrative platform for transcriptional regulation studies, from peak calling, correlation and association studies, expression analyses, to motif discovery.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cistrome: an integrative platform for transcriptional regulation studies.
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS.
Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

CCAT – Combinatorial Code Analysis Tool for Transcriptional Regulation

CCAT

:: DESCRIPTION

CCAT is a software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs). The CCAT package also includes accompanying tools to cluster similar Position weight matrix (PWMs) of different TFs into clusters; and search PWMs on multiple genome alignments for conserved motif instances.

::DEVELOPER

Peng Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 CCAT

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Mar;42(5):2833-47. doi: 10.1093/nar/gkt1302. Epub 2013 Dec 23.
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.
Jiang P1, Singh M.

GBNet – Tool for Deciphering the “grammar” of Transcriptional Regulation

GBNet

:: DESCRIPTION

GBNet (Gibbs sampler enhanced Bayesian Network) is designed to search for enriched sequence constraints such as a motif pair and positional preference of motif in a group of co-regulated genes.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Complier

:: DOWNLOAD

 GBNet

:: MORE INFORMATION

Citation

Li Shen, Jie Liu, Wei Wang,
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach,
BMC Bioinformatics 2008, 9:395.

TAMO 20120321 – Analyze Transcriptional Regulation using DNA-sequence Motifs

TAMO 20120321

:: DESCRIPTION

TAMO  (Tools for Analysis of MOtifs) is developed around a unified motif representation of a position-specific scoring matrix (PSSM). Motif objects may be assembled from IUPAC-ambiguity codes, multiple sequence alignments, averages of other motifs, and matrices of frequencies or log-likelihood values. Motifs can printed, concatenated, indexed and sliced like text strings, or rendered as sequence logos. They can also be randomized, reverse-complemented, and recomputed using different assumptions about background base frequencies. Motifs can also store and report information about their origin, information content, and score. Finally, motifs can scan DNA sequences for instances of matching sites.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 TAMO

:: MORE INFORMATION

Citation:

D. Benjamin Gordon, Lena Nekludova, Scott McCallum and Ernest Fraenke
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
Bioinformatics. 2005 Jul 15;21(14):3164-5.