Organism : Bacillus cereus ATCC14579 | Module List :
BC3826

Transcription pleiotropic repressor codY (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3826
(Mouseover regulator name to see its description)

BC3826 is regulated by 28 influences and regulates 39 modules.
Regulators for BC3826 (28)
Regulator Module Operator
BC0059 49 tf
BC0114 49 tf
BC0122 49 tf
BC0230 49 tf
BC0518 49 tf
BC2770 49 tf
BC3207 49 tf
BC3653 49 tf
BC3690 49 tf
BC3814 49 tf
BC3826 49 tf
BC3982 49 tf
BC4057 49 tf
BC4499 49 tf
BC0122 69 tf
BC0518 69 tf
BC0613 69 tf
BC1363 69 tf
BC1884 69 tf
BC2672 69 tf
BC3813 69 tf
BC3814 69 tf
BC3826 69 tf
BC4076 69 tf
BC4314 69 tf
BC4525 69 tf
BC5265 69 tf
BC5339 69 tf

Warning: BC3826 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
4018 6.50e+01 CAacAcgGG
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4019 8.50e+03 GAGGTGAG
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4058 1.30e+02 CcGCaCGC
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4059 4.10e+02 tC.tt.gaaGGgtACcA.tT
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BC3826

BC3826 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
Module neighborhood information for BC3826

BC3826 has total of 32 gene neighbors in modules 49, 69
Gene neighbors (32)
Gene Common Name Description Module membership
BC0020 BC0020 None 69, 198
BC0021 BC0021 Deoxyguanosine kinase (NCBI ptt file) 69, 458
BC0060 BC0060 Polysaccharides export protein (NCBI ptt file) 49, 222
BC0061 BC0061 MazG protein (NCBI ptt file) 49, 425
BC0062 BC0062 Heat shock protein 15 (NCBI ptt file) 49, 222
BC0063 BC0063 hypothetical protein (NCBI ptt file) 49, 222
BC1287 BC1287 Spermidine/putrescine transport system permease protein potB (NCBI ptt file) 49, 510
BC1288 BC1288 Spermidine/putrescine transport system permease protein potC (NCBI ptt file) 49, 510
BC1504 BC1504 GTP-binding protein (NCBI ptt file) 49, 259
BC1505 BC1505 Glycerol-3-phosphate dehydrogenase [NAD(P)+] (NCBI ptt file) 49, 259
BC2102 BC2102 hypothetical protein (NCBI ptt file) 69, 236
BC2103 BC2103 ATP-dependent RNA helicase (NCBI ptt file) 69, 236
BC3826 BC3826 Transcription pleiotropic repressor codY (NCBI ptt file) 49, 69
BC3827 BC3827 ATP-dependent hsl protease ATP-binding subunit hslU (NCBI ptt file) 49, 69
BC3828 BC3828 ATP-dependent protease hslV (NCBI ptt file) 49, 69
BC3829 BC3829 Integrase/recombinase (XerC/CodV family) (NCBI ptt file) 49, 69
BC3914 BC3914 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (NCBI ptt file) 49, 143
BC4283 BC4283 ATP-dependent RNA helicase (NCBI ptt file) 69, 75
BC4331 BC4331 Shikimate 5-dehydrogenase (NCBI ptt file) 49, 259
BC4375 BC4375 Uridine kinase (NCBI ptt file) 49, 458
BC4376 BC4376 Protease (NCBI ptt file) 49, 458
BC4377 BC4377 Collagenase (NCBI ptt file) 49, 510
BC4444 BC4444 Rod shape-determining protein mreD (NCBI ptt file) 49, 192
BC5266 BC5266 Heteropolysaccharide repeat unit export protein (NCBI ptt file) 69, 458
BC5267 BC5267 Glycosyltransferase (NCBI ptt file) 69, 458
BC5268 BC5268 Secreted polysaccharide polymerase (NCBI ptt file) 69, 458
BC5269 BC5269 Amylovoran biosynthesis AmsK (NCBI ptt file) 69, 458
BC5270 BC5270 Undecaprenyl-phosphate galactosephosphotransferase (NCBI ptt file) 69, 458
BC5271 BC5271 UDP-N-acetylglucosamine 4-epimerase (NCBI ptt file) 69, 458
BC5272 BC5272 Carbamoyl-phosphate synthase small chain (NCBI ptt file) 69, 458
BC5273 BC5273 UDP-bacillosamine synthetase (NCBI ptt file) 69, 458
BC5473 BC5473 IG hypothetical 15508 (NCBI ptt file) 49, 476
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BC3826
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend