Promoter features related to tissue specificity as measured by Shannon entropy
-
* Corresponding author: Jonathan Schug jschug@pcbi.upenn.edu
Genome Biology 2005, 6:R33 doi:10.1186/gb-2005-6-4-r33
Accesses
- Last 30 days: 138 accesses
- Last 365 days: 1756 accesses
- All time: 14372 accesses
Cited by
BioMed Central: 18 citations
|
Research article
Expression cartography of human tissues using self organizing maps Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder BMC Bioinformatics 2011, 12:306 (27 July 2011) |
|
Research article
YY1 is autoregulated through its own DNA-binding sites Jeong Kim, Sungryul Yu, Joomyeong Kim BMC Molecular Biology 2009, 10:85 (27 August 2009) Levels of the transcription factor Yin Yang 1 (YY1), which controls many genes and biological processes in vertebrates, is self-regulated through internal DNA-binding sites.
|
|
Research
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler Genome Biology 2009, 10:R73 (9 July 2009) A map of transcription start sites across the |
|
Research article
Maternal diabetes alters transcriptional programs in the developing embryo Gabriela Pavlinkova, J Michael Salbaum, Claudia Kappen BMC Genomics 2009, 10:274 (18 June 2009) |
|
Research article
Mara E Pitulescu, Martin Teichmann, Lingfei Luo, Michael Kessel BMC Biochemistry 2009, 10:16 (10 June 2009) A novel transcriptional regulator, isoform 2 of the TATA-binding protein-like factor-interacting protein (TIPT2), binds to the cell cycle regulatory protein geminin, and together they cooperate with chromatin associated factors and the basal transcription machinery to activate transcription synergistically.
|
|
Research article
Conservation of core gene expression in vertebrate tissues Esther T Chan, Gerald T Quon, Gordon Chua, Tomas Babak, Miles Trochesset, Ralph A Zirngibl, Jane Aubin, Michael JH Ratcliffe, Andrew Wilde, Michael Brudno, Quaid D Morris, Timothy R Hughes Journal of Biology 2009, 8:33 (16 April 2009) High conservation of tissue-specific expression is found across vertebrates yet there is a lack of conservation in common regulatory sequences/signatures.
|
|
Research article
Sample entropy analysis of cervical neoplasia gene-expression signatures Shaleen K Botting, Jerome P Trzeciakowski, Michelle F Benoit, Salama A Salama, Concepcion R Diaz-Arrastia BMC Bioinformatics 2009, 10:66 (20 February 2009) Patterns of gene expression indicative of cervical cancer can be detected using approximate entropy analysis of microarray datasets to identify genes displaying minimum variation in control tissue versus maximum variation in cancerous samples.
|
|
Research article
Qianqian Zhu, Marc S Halfon BMC Genomics 2009, 10:9 (7 January 2009) |
|
Research
Identification of transcripts with enriched expression in the developing and adult pancreas Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven JM Jones, Marco A Marra, Cheryl D Helgason Genome Biology 2008, 9:R99 (14 June 2008) The expression profile of different developmental stages of the murine pancreas and predictions of transcription factor interactions, provides a framework for pancreas regulatory networks and development. |
|
Research article
Prediction and analysis of nucleosome exclusion regions in the human genome Ahmed Radwan, Akmal Younis, Peter Luykx, Sawsan Khuri BMC Genomics 2008, 9:186 (22 April 2008) |
|
Research article
Links between core promoter and basic gene features influence gene expression Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, Rivka Dikstein BMC Genomics 2008, 9:92 (25 February 2008) |
|
Research Article
Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information Arvind Rao, Alfred O Hero, David J States, James Engel EURASIP Journal on Bioinformatics and Systems Biology 2007, 2007:13853 (24 December 2007) This article is part of a collection on Information Theoretic... |
|
Research
Housekeeping genes tend to show reduced upstream sequence conservation Domènec Farré, Nicolás Bellora, Loris Mularoni, Xavier Messeguer, M Mar Albà Genome Biology 2007, 8:R140 (13 July 2007) Mammalian housekeeping genes show significantly lower promoter sequence conservation, especially upstream of position -500 with respect to the transcription start site, than genes expressed in a subset of tissues. |
|
Method
Boosting with stumps for predicting transcription start sites Xiaoyue Zhao, Zhenyu Xuan, Michael Q Zhang Genome Biology 2007, 8:R17 (2 February 2007) CoreBoost applies a boosting technique to select important features for predicting core promoters with diverse patterns. |
|
Software
REEF: searching REgionally Enriched Features in genomes Alessandro Coppe, Gian Antonio Danieli, Stefania Bortoluzzi BMC Bioinformatics 2006, 7:453 (16 October 2006) |
|
Research
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters Jasmina Ponjavic, Boris Lenhard, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Albin Sandelin Genome Biology 2006, 7:R78 (17 August 2006) Investigations of the spacing between TATA box and transcription start site in mouse core promoters reveals a coupling of spacing to tissue specificity. |
|
Research article
ROKU: a novel method for identification of tissue-specific genes Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, Kentaro Shimizu BMC Bioinformatics 2006, 7:294 (12 June 2006) |
|
Method
A classification based framework for quantitative description of large-scale microarray data Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky Genome Biology 2006, 7:R32 (20 April 2006) A new classification-based framework is presented that allows quantitative description of microarray data in terms of significance of co-expression within any gene group and condition-specific gene class activity. |