Organism : Bacillus cereus ATCC14579 | Module List :
BC3903

RNA polymerase sigma-G factor (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
RNA polymerase kegg/ kegg pathway
spore_sigG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3903
(Mouseover regulator name to see its description)

BC3903 is regulated by 23 influences and regulates 33 modules.
Regulators for BC3903 (23)
Regulator Module Operator
BC0230 520 tf
BC0742 520 tf
BC2469 520 tf
BC2760 520 tf
BC2964 520 tf
BC3095 520 tf
BC3868 520 tf
BC5402 520 tf
BC0047 136 tf
BC0477 136 tf
BC0566 136 tf
BC0648 136 tf
BC0961 136 tf
BC1083 136 tf
BC1335 136 tf
BC2166 136 tf
BC2517 136 tf
BC3903 136 tf
BC3904 136 tf
BC4336 136 tf
BC4425 136 tf
BC4930 136 tf
BC5200 136 tf

Warning: BC3903 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
4188 3.60e+02 AgGGgGaa
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4189 6.30e+01 TCtCTTTttTC
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4950 1.10e-02 aA.aAgaGGgg
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4951 5.00e+03 ggTGGtTgg
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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 BC3903

BC3903 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
RNA polymerase kegg/ kegg pathway
spore_sigG tigr/ tigrfam
Module neighborhood information for BC3903

BC3903 has total of 40 gene neighbors in modules 136, 520
Gene neighbors (40)
Gene Common Name Description Module membership
BC0239 BC0239 ABC transporter ATP-binding protein uup (NCBI ptt file) 68, 136
BC0386 BC0386 hypothetical protein (NCBI ptt file) 241, 520
BC0511 BC0511 Glutamate synthase [NADPH] large chain (NCBI ptt file) 358, 520
BC1063 BC1063 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 59, 520
BC1152 BC1152 Asparagine synthetase (NCBI ptt file) 136, 217
BC1248 BC1248 NADH oxidase (NOXASE) (NCBI ptt file) 136, 181
BC1928 BC1928 Branched-chain amino acid transport ATP-binding protein livG (NCBI ptt file) 334, 520
BC1930 BC1930 Branched-chain amino acid transport system permease protein livH (NCBI ptt file) 206, 520
BC1979 BC1979 Siderophore biosynthesis protein (NCBI ptt file) 46, 520
BC1981 BC1981 Acyl carrier protein (NCBI ptt file) 46, 520
BC1982 BC1982 hypothetical protein (NCBI ptt file) 504, 520
BC2005 BC2005 GTPase (NCBI ptt file) 23, 520
BC2109 BC2109 ECF-type sigma factor negative effector (NCBI ptt file) 327, 520
BC2380 BC2380 hypothetical Membrane Spanning Protein (NCBI ptt file) 136, 174
BC2541 BC2541 ABC transporter ATP-binding protein (NCBI ptt file) 136, 351
BC2545 BC2545 hypothetical protein (NCBI ptt file) 136, 217
BC2636 BC2636 hypothetical protein (NCBI ptt file) 46, 520
BC2664 BC2664 Penicillin-binding protein (NCBI ptt file) 73, 520
BC2745 BC2745 hypothetical protein (NCBI ptt file) 136, 181
BC2800 BC2800 hypothetical Cytosolic Protein (NCBI ptt file) 136, 168
BC3280 BC3280 hypothetical protein (NCBI ptt file) 136, 217
BC3312 BC3312 3-Oxoadipate enol-lactonase (NCBI ptt file) 377, 520
BC3325 BC3325 hypothetical protein (NCBI ptt file) 136, 309
BC3345 BC3345 Collagen-like triple helix repeat protein (NCBI ptt file) 21, 520
BC3502 BC3502 IG hypothetical 17676 (NCBI ptt file) 189, 520
BC3710 BC3710 None 376, 520
BC3903 BC3903 RNA polymerase sigma-G factor (NCBI ptt file) 136, 520
BC3905 BC3905 Sporulation sigma-E factor processing peptidase (NCBI ptt file) 17, 520
BC4154 BC4154 hypothetical Membrane Associated Protein (NCBI ptt file) 136, 174
BC4172 BC4172 Stage IV sporulation protein B (NCBI ptt file) 60, 136
BC4188 BC4188 Stage III sporulation protein AF (NCBI ptt file) 136, 307
BC4296 BC4296 hypothetical protein (NCBI ptt file) 125, 136
BC4420 BC4420 SpoVID-dependent spore coat assembly factor SafA (NCBI ptt file) 21, 136
BC4447 BC4447 DNA repair protein radC (NCBI ptt file) 136, 464
BC4663 BC4663 Proline iminopeptidase (NCBI ptt file) 136, 174
BC4731 BC4731 Spore germination protein IA (NCBI ptt file) 136, 205
BC4732 BC4732 Spore germination protein IB (NCBI ptt file) 136, 205
BC4912 BC4912 hypothetical Membrane Spanning Protein (NCBI ptt file) 136, 309
BC5166 BC5166 hypothetical protein (NCBI ptt file) 136, 351
BC5224 BC5224 Cytochrome d ubiquinol oxidase subunit I (NCBI ptt file) 378, 520
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 BC3903
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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