Swissregulon is a database with genome-wide annotations of regulatory sites. All predictions are made using the PhyloGibbs algorithm. The annotations are visualized using the Gbrowse genome browser. At the moment SwissRegulon contains annotations for Saccharomyces cerevisiae only.
http://swissregulon.unibas.ch/
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SwissRegulon | swissregulon.unibas.ch Reviews
https://swissregulon.unibas.ch
Swissregulon is a database with genome-wide annotations of regulatory sites. All predictions are made using the PhyloGibbs algorithm. The annotations are visualized using the Gbrowse genome browser. At the moment SwissRegulon contains annotations for Saccharomyces cerevisiae only.
swissregulon.unibas.ch
SwissRegulon
http://swissregulon.unibas.ch/fcgi/sr/fantom4
Swiss Institute of Bioinformatics. Motevo predictions for CAGE promoters. Motevo predictions for REFSEQ promoters. Regulatory motifs (weight matrices). Association of regulatory motifs with TFs. Predicted regulatory edges for CAGE promoters. Predicted regulatory edges for REFSEQ promoters. Multispecies alignments of CAGE promoters. Multispecies alignments of REFSEQ promoters.
SwissRegulon
http://swissregulon.unibas.ch/fcgi/sr/documentation
Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Prediction of transcription factor binding sites with Motevo algorithm:. Finding regulatory elements and regulatory motifs: a general probabilistic framework. 2007 Sep 27; 8 Suppl 6:S4. Annotating of promoteroms (transcription start sites, transcription start clusters and transcription start regions):. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
Prediction of two-component interactions
http://swissregulon.unibas.ch/cgi-bin/TCS.pl
Prediction of Interaction Specificity in Two-component Systems. Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Lukas Burger and Erik van Nimwegen. Molecular Systems Biology 4:165. Please choose a bacterium to see the scores for a certain orphan kinase or regulator. Agrobacterium tumefaciens C58 Cereon. Agrobacterium tumefaciens C58 UWash. Anabaena variabilis ATCC 29413. Anaplasma marginale St Maries. Aster yellows witches-broom phytoplasma AYWB.
SwissRegulon
http://swissregulon.unibas.ch/fcgi/sr/swissregulon
Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including:. Experimentally determined binding sites reported in the literature. Known sequence-specificities of transcription factors. ChIP-chip and ChIP-seq data. Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs.
SwissRegulon
http://swissregulon.unibas.ch/fcgi/sr/publications
Swiss Institute of Bioinformatics. The transcriptional landscape of the mammalian genome. P Carninci, T. Kasukawa, S. Katayama, J. Gough, M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells and others. Science, 2005, 309(5740), 1559- 1563. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. R Siddharthan, E. Siggia and E. Van Nimwegen. PLoS computational biology, 2005, 1(7), e67. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.
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autosome.ru Opera House: bioinformatics tools on the web
http://opera.autosome.ru/perfectosape
HOCOMOCO collection of TFBS motifs. EpiFactors database for epigenetic regulators. PERFECTOS-APE: PrEdicting Regulatory Functional Effect by Approximate P-value Estimation. Software predicts possible regulatory role of single nucleotide variants (SNVs) or polymorphisms (SNPs). The main idea is that SNVs may be located directly within transcription factor binding sites and different SNV alleles can change binding affinity. Allows testing SNVs against several publically available TFBS models: HOCOMOCO-10.
ExPASy: SIB Bioinformatics Resource Portal - Categories
http://www.expasy.org/genomics
Query within a category:. Query a specific database:. Protein sequences and identification. Sequence sites, features and motifs. No support from the ExPASy Team). Bull; collection of eukaryotic promoters • [more]. Bull; Hierarchical catalog of eukaryotic orthologs • [more]. Bull; annotations of regulatory sites • [more]. Bull; SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intu...Bull;...
autosome.ru Opera House: bioinformatics tools on the web
http://opera.autosome.ru/perfectosape/description
HOCOMOCO collection of TFBS motifs. EpiFactors database for epigenetic regulators. PERFECTOS-APE: PrEdicting Regulatory Functional Effect by Approximate P-value Estimation. Software predicts possible regulatory role of single nucleotide variants (SNVs) or polymorphisms (SNPs). The main idea is that SNVs may be located directly within transcription factor binding sites and different SNV alleles can change binding affinity. Allows testing SNVs against several publically available TFBS models: HOCOMOCO-10.
FANTOM 4 | Home Page
http://fantom.gsc.riken.jp/4
Go to current FANTOM site. Functional Annotation of the Mammalian Genome. The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. Post this site to:.
FANTOM - Views
http://fantom.gsc.riken.jp/views
Resources for visualizing FANTOM data. A new data integration, data processing, and expression enhanced visualization system with secured data upload and sharing designed for big data genomics projects (FANTOM5, FANTOM4, FANTOM3, ENCODE). Primary data visualization system for FANTOM5. Kanamori-Katayama et al, 2011.6. Supplemental materials for Kanamori-Katayama et al, 2011. A analysis tool used to identify patterns in FANTOM5 data by building network visualizations of correlation matrices. Mouse mm9 asse...
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SwissRegulon
Swiss Institute of Bioinformatics. Search mammal promoters and motifs:. Welcome to SwissRegulon portal. A repository of datbases and bioinformatic tools related to transcription regulatory processes and includes:. A database of genome-wide annotations of regulatory sites. We currently have annotations for 17 prokaryotes and 3 eukaroytes in our collection. The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data.
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