Organism : Bacillus cereus ATCC14579 | Module List :
BC4170

Stage 0 sporulation protein A (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
Response regulator of citrate/malate metabolism cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
calcium ion binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of sporulation resulting in formation of a cellular spore go/ biological_process
detection of stimulus involved in sensory perception go/ biological_process
Two-component system kegg/ kegg pathway
spore_0_A tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4170
(Mouseover regulator name to see its description)

BC4170 is regulated by 26 influences and regulates 19 modules.
Regulators for BC4170 (26)
Regulator Module Operator
BC0265 350 tf
BC0880 350 tf
BC1282 350 tf
BC2358 350 tf
BC2549 350 tf
BC3868 350 tf
BC4101 350 tf
BC4124 350 tf
BC4170 350 tf
BC4174 350 tf
BC4256 350 tf
BC5332 350 tf
BC5339 350 tf
BC0806 380 tf
BC1282 380 tf
BC1387 380 tf
BC3922 380 tf
BC3976 380 tf
BC4170 380 tf
BC4174 380 tf
BC4240 380 tf
BC4256 380 tf
BC4425 380 tf
BC4826 380 tf
BC5409 380 tf
BC5483 380 tf

Warning: BC4170 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
4610 1.20e-02 aGGAGGaa
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4611 1.00e+02 AcTCcC
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4670 1.90e-01 AAgaaaAG.Gg
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4671 4.50e+04 GcaGGAcG
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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 BC4170

BC4170 is enriched for 11 functions in 3 categories.
Module neighborhood information for BC4170

BC4170 has total of 30 gene neighbors in modules 350, 380
Gene neighbors (30)
Gene Common Name Description Module membership
BC0066 BC0066 S1-type RNA-binding domain (NCBI ptt file) 275, 350
BC0220 BC0220 Molybdenum transport system permease protein modB (NCBI ptt file) 28, 380
BC0221 BC0221 Molybdate-binding protein (NCBI ptt file) 296, 380
BC0546 BC0546 23S rRNA methyltransferase (NCBI ptt file) 90, 380
BC0695 BC0695 Cytochrome aa3 quinol oxidase polypeptide IV (NCBI ptt file) 188, 380
BC0738 BC0738 hypothetical protein (NCBI ptt file) 296, 380
BC0805 BC0805 outer surface protein (NCBI ptt file) 7, 380
BC0880 BC0880 putative transcriptional regulator (NCBI ptt file) 226, 350
BC1021 BC1021 CMP-binding factor (NCBI ptt file) 350, 380
BC1048 BC1048 IG hypothetical 17707 (NCBI ptt file) 226, 350
BC1282 BC1282 SinR protein (NCBI ptt file) 350, 380
BC1387 BC1387 Transcriptional regulator, MarR family (NCBI ptt file) 28, 380
BC1562 BC1562 Cell division protein DIVIVA (NCBI ptt file) 166, 380
BC1603 BC1603 Cold shock protein (NCBI ptt file) 296, 350
BC2358 BC2358 Cold shock protein (NCBI ptt file) 70, 350
BC2844 BC2844 None 129, 380
BC3539 BC3539 Cold shock protein (NCBI ptt file) 70, 350
BC3680 BC3680 hypothetical Exported Protein (NCBI ptt file) 226, 350
BC3957 BC3957 hypothetical protein (NCBI ptt file) 350, 477
BC4168 BC4168 hypothetical protein (NCBI ptt file) 126, 350
BC4170 BC4170 Stage 0 sporulation protein A (NCBI ptt file) 350, 380
BC4174 BC4174 Arginine repressor, argR (NCBI ptt file) 350, 380
BC4182 BC4182 hypothetical Cytosolic Protein (NCBI ptt file) 191, 350
BC4197 BC4197 Protein Translation Elongation Factor P (EF-P) (NCBI ptt file) 187, 350
BC4859 BC4859 Cold shock protein (NCBI ptt file) 70, 350
BC4861 BC4861 hypothetical protein (NCBI ptt file) 90, 380
BC4917 BC4917 BioY protein (NCBI ptt file) 103, 350
BC5201 BC5201 UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) 372, 380
BC5356 BC5356 methionine aminopeptidase (RefSeq) 350, 380
BC5409 BC5409 Catabolite gene activator (NCBI ptt file) 187, 380
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 BC4170
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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