Organism : Bacillus cereus ATCC14579 | Module List :
BC2122

Transcription regulator, Crp family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases 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 BC2122
(Mouseover regulator name to see its description)

BC2122 is regulated by 28 influences and regulates 19 modules.
Regulators for BC2122 (28)
Regulator Module Operator
BC0099 290 tf
BC0473 290 tf
BC0806 290 tf
BC2122 290 tf
BC3095 290 tf
BC3826 290 tf
BC3922 290 tf
BC4240 290 tf
BC4708 290 tf
BC5205 290 tf
BC0099 266 tf
BC0356 266 tf
BC0410 266 tf
BC0806 266 tf
BC1302 266 tf
BC1622 266 tf
BC1884 266 tf
BC2122 266 tf
BC2444 266 tf
BC2979 266 tf
BC3404 266 tf
BC3826 266 tf
BC3868 266 tf
BC3922 266 tf
BC4057 266 tf
BC4672 266 tf
BC4842 266 tf
BC5402 266 tf

Warning: BC2122 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
4448 1.70e-02 gaatgaAaaaAgagaGcggattac
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4449 1.40e+02 AGGGgGgA
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4496 6.50e+01 AAgGtTtTCaT
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4497 1.50e+04 GGGAGAGG
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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 BC2122

BC2122 is enriched for 4 functions in 3 categories.
Module neighborhood information for BC2122

BC2122 has total of 36 gene neighbors in modules 266, 290
Gene neighbors (36)
Gene Common Name Description Module membership
BC0023 BC0023 Cytosine deaminase (NCBI ptt file) 134, 266
BC0421 BC0421 Anaerobic C4-dicarboxylate transporter (NCBI ptt file) 290, 396
BC0482 BC0482 PTS system, N-acetylglucosamine-specific IIBC component (NCBI ptt file) 103, 290
BC0502 BC0502 hypothetical Cytosolic Protein (NCBI ptt file) 266, 389
BC0773 BC0773 Fructokinase (NCBI ptt file) 290, 396
BC0806 BC0806 Transcription antiterminator, BglG family (NCBI ptt file) 7, 290
BC0893 BC0893 Sulfate transporter (NCBI ptt file) 266, 290
BC1452 BC1452 hypothetical Membrane Spanning Protein (NCBI ptt file) 198, 290
BC1496 BC1496 L-asparaginase (NCBI ptt file) 290, 382
BC1671 BC1671 Flagellar basal-body rod protein flgG (NCBI ptt file) 266, 462
BC2122 BC2122 Transcription regulator, Crp family (NCBI ptt file) 266, 290
BC2202 BC2202 Cytochrome c oxidase Cu(A) center assembly protein (NCBI ptt file) 198, 290
BC2205 BC2205 Acetyltransferase (NCBI ptt file) 266, 341
BC2206 BC2206 hypothetical protein (NCBI ptt file) 266, 290
BC2211 BC2211 hypothetical protein (NCBI ptt file) 266, 401
BC2257 BC2257 hypothetical protein (NCBI ptt file) 266, 462
BC2258 BC2258 Serine/threonine protein kinase (NCBI ptt file) 266, 462
BC2259 BC2259 Sporulation-control protein (NCBI ptt file) 266, 290
BC2260 BC2260 Phosphatidylglycerophosphatase B (NCBI ptt file) 266, 290
BC2333 BC2333 hypothetical protein (NCBI ptt file) 214, 266
BC2354 BC2354 Protoporphyrinogen oxidase (NCBI ptt file) 198, 290
BC2462 BC2462 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 72, 266
BC3505 BC3505 hypothetical protein (NCBI ptt file) 213, 266
BC3662 BC3662 Cytochrome c-type biogenesis protein ccdA (NCBI ptt file) 290, 481
BC3722 BC3722 hypothetical Membrane Spanning Protein (NCBI ptt file) 198, 290
BC4008 BC4008 hypothetical protein (NCBI ptt file) 266, 290
BC4083 BC4083 Guanine-hypoxanthine permease (NCBI ptt file) 283, 290
BC4637 BC4637 Acetate kinase (NCBI ptt file) 266, 290
BC4959 BC4959 4-nitrophenylphosphatase (NCBI ptt file) 266, 290
BC5034 BC5034 Methyl-accepting chemotaxis protein (NCBI ptt file) 214, 266
BC5258 BC5258 Phosphoglycerate transporter protein (NCBI ptt file) 100, 290
BC5260 BC5260 hypothetical Exported Protein (NCBI ptt file) 283, 290
BC5315 BC5315 Uracil phosphoribosyltransferase (NCBI ptt file) 266, 396
BC5444 BC5444 Nitric oxide synthase (NCBI ptt file) 187, 290
BC5452 BC5452 GMP reductase (NCBI ptt file) 266, 290
BC5468 BC5468 Adenylosuccinate synthetase (NCBI ptt file) 290, 477
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 BC2122
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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