Organism : Bacillus subtilis | Module List :
BSU40870 ccpB

transcriptional repressor of carbon supply (LacI family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40870
(Mouseover regulator name to see its description)

BSU40870 is regulated by 37 influences and regulates 7 modules.
Regulators for BSU40870 ccpB (37)
Regulator Module Operator
BSU00230 257 tf
BSU02070 257 tf
BSU04100 257 tf
BSU05060 257 tf
BSU06860 257 tf
BSU07820 257 tf
BSU09650 257 tf
BSU11500 257 tf
BSU13150 257 tf
BSU23100 257 tf
BSU23520 257 tf
BSU27080 257 tf
BSU32420 257 tf
BSU34220 257 tf
BSU34380 257 tf
BSU35110 257 tf
BSU35430 257 tf
BSU36630 257 tf
BSU37080 257 tf
BSU40870 257 tf
BSU40990 257 tf
BSU02160 301 tf
BSU03560 301 tf
BSU05420 301 tf
BSU06700 301 tf
BSU07390 301 tf
BSU13670 301 tf
BSU13870 301 tf
BSU17850 301 tf
BSU20820 301 tf
BSU21700 301 tf
BSU26220 301 tf
BSU26320 301 tf
BSU26730 301 tf
BSU29000 301 tf
BSU36600 301 tf
BSU39850 301 tf

Warning: BSU40870 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
5454 7.70e-02 gAtggaggAtGATgAaag
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5455 3.20e+01 a.aAAA.aGCT.GAa
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5540 8.70e+00 TAtaAgAAggaGC
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5541 4.80e+00 gAaAGgaG
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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 BSU40870

BSU40870 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU40870

BSU40870 has total of 29 gene neighbors in modules 257, 301
Gene neighbors (29)
Gene Common Name Description Module membership
BSU00450 sspF small acid-soluble spore protein (alpha/beta-type SASP) (RefSeq) 282, 301
BSU02240 mpr extracellular metalloprotease (RefSeq) 257, 304
BSU02560 ycbM two-component sensor histidine kinase [YcbL] (RefSeq) 219, 301
BSU04780 ydcI putative RNA helicase (RefSeq) 219, 301
BSU06550 yecA putative amino acid/polyamine permease (RefSeq) 130, 301
BSU09210 yhcT putative RNA pseudouridine synthase (RefSeq) 200, 301
BSU10160 yhgE putative methyl-accepting protein (RefSeq) 178, 301
BSU12190 yjhB putative ADP-ribose pyrophosphatase (RefSeq) 180, 257
BSU14320 yknU putative ABC transporter (ATP-binding protein) (RefSeq) 257, 304
BSU17640 alrB alanine racemase (RefSeq) 246, 301
BSU17770 yndF putative spore germination lipoprotein (RefSeq) 44, 301
BSU17910 yneF hypothetical protein (RefSeq) 142, 301
BSU21000 yonT hypothetical protein; phage SPbeta (RefSeq) 110, 301
BSU21820 thyA thymidylate synthase (RefSeq) 270, 301
BSU22860 yphA putative integral inner membrane protein (RefSeq) 257, 365
BSU23329 ypuC 149, 257
BSU25990 yqbS conserved hypothetical protein; skin element (RefSeq) 178, 301
BSU26850 yrpG putative oxidoreductase (RefSeq) 206, 301
BSU32410 pucH allantoinase (RefSeq) 231, 257
BSU32420 pucR transcriptional regulator of the purine degradation operon (RefSeq) 257, 258
BSU32720 yurZ hypothetical protein (RefSeq) 246, 301
BSU33390 yvgM putative molybdenum transport permease (RefSeq) 177, 301
BSU35060 cypX putative monooxygenase (cytochrome P450) (RefSeq) 257, 406
BSU35070 yvmC hypothetical protein (RefSeq) 257, 406
BSU36940 ywlD putative integral inner membrane protein UPF0059 DUF0204 family (RefSeq) 84, 301
BSU40850 maa maltose O-acetyltransferase (RefSeq) 257, 285
BSU40860 yyaH putative lyase (RefSeq) 149, 257
BSU40870 ccpB transcriptional repressor of carbon supply (LacI family) (RefSeq) 257, 301
BSU40880 exoAA apurinic/apyrimidinic endonuclease (RefSeq) 89, 301
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 BSU40870
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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