Organism : Bacillus cereus ATCC14579 | Module List :
BC3589

RNA polymerase ECF-type sigma factor (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III 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
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3589
(Mouseover regulator name to see its description)

BC3589 is regulated by 33 influences and regulates 13 modules.
Regulators for BC3589 (33)
Regulator Module Operator
BC0123 163 tf
BC0473 163 tf
BC0598 163 tf
BC0882 163 tf
BC0953 163 tf
BC0993 163 tf
BC1037 163 tf
BC2217 163 tf
BC2386 163 tf
BC2914 163 tf
BC3069 163 tf
BC3400 163 tf
BC3493 163 tf
BC3497 163 tf
BC3589 163 tf
BC3653 163 tf
BC3693 163 tf
BC4073 163 tf
BC5361 163 tf
BC0647 25 tf
BC0954 25 tf
BC1850 25 tf
BC1884 25 tf
BC2386 25 tf
BC2680 25 tf
BC3033 25 tf
BC3069 25 tf
BC3084 25 tf
BC3175 25 tf
BC3434 25 tf
BC3589 25 tf
BC3903 25 tf
BC4053 25 tf

Warning: BC3589 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
3972 6.20e+02 aaag.aGgaA.acaa
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3973 8.30e+00 AAAGGAga
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4242 2.20e-07 AagggGAg
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4243 7.20e+02 gagagtacttctctTcctTttTTa
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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 BC3589

BC3589 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III 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
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for BC3589

BC3589 has total of 71 gene neighbors in modules 25, 163
Gene neighbors (71)
Gene Common Name Description Module membership
BC0298 BC0298 Two-component response regulator (NCBI ptt file) 163, 281
BC0299 BC0299 Two component system histidine kinase (NCBI ptt file) 163, 308
BC0349 BC0349 hypothetical protein (NCBI ptt file) 20, 163
BC0396 BC0396 ATPase (NCBI ptt file) 25, 84
BC0455 BC0455 hypothetical Membrane Spanning Protein (NCBI ptt file) 163, 293
BC0456 BC0456 Signal peptidase I (NCBI ptt file) 146, 163
BC0484 BC0484 hypothetical protein (NCBI ptt file) 9, 25
BC0627 BC0627 hypothetical protein (NCBI ptt file) 25, 174
BC0647 BC0647 RNA polymerase ECF-type sigma factor (NCBI ptt file) 25, 162
BC0783 BC0783 Spore germination protein, gerC family (NCBI ptt file) 25, 131
BC0810 BC0810 hypothetical protein (NCBI ptt file) 25, 255
BC0886 BC0886 hydrolase (HAD superfamily) (NCBI ptt file) 25, 402
BC1016 BC1016 hypothetical protein (NCBI ptt file) 158, 163
BC1073 BC1073 hypothetical protein (NCBI ptt file) 85, 163
BC1096 BC1096 hypothetical protein (NCBI ptt file) 25, 308
BC1121 BC1121 hypothetical protein (NCBI ptt file) 163, 327
BC1127 BC1127 Malate synthase (NCBI ptt file) 163, 218
BC1189 BC1189 Integral membrane protein (NCBI ptt file) 25, 158
BC1205 BC1205 Methyltransferase (NCBI ptt file) 25, 397
BC1274 BC1274 hypothetical protein (NCBI ptt file) 25, 128
BC1480 BC1480 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 25, 96
BC1604 BC1604 hypothetical protein (NCBI ptt file) 25, 330
BC1607 BC1607 Fatty acid hydroxylase FAH1P (NCBI ptt file) 163, 395
BC1691 BC1691 Phosphoglycerate mutase (NCBI ptt file) 25, 141
BC1731 BC1731 RNA polymerase ECF-type sigma factor (NCBI ptt file) 25, 485
BC1737 BC1737 Cardiolipin synthetase (NCBI ptt file) 25, 162
BC1800 BC1800 Two-component response regulator vanR (NCBI ptt file) 97, 163
BC2162 BC2162 Methyltransferase (NCBI ptt file) 25, 238
BC2240 BC2240 Magnesium and cobalt efflux protein corC (NCBI ptt file) 163, 258
BC2315 BC2315 DinB protein (NCBI ptt file) 63, 163
BC2326 BC2326 Oligopeptide transport system permease protein oppB (NCBI ptt file) 163, 209
BC2332 BC2332 hypothetical protein (NCBI ptt file) 163, 299
BC2348 BC2348 Acetyltransferase (NCBI ptt file) 163, 453
BC2412 BC2412 ABC transporter permease protein (NCBI ptt file) 163, 253
BC2424 BC2424 hypothetical protein (NCBI ptt file) 25, 415
BC2482 BC2482 hypothetical Cytosolic Protein (NCBI ptt file) 163, 299
BC2494 BC2494 Aminoglycoside N6'-acetyltransferase (NCBI ptt file) 146, 163
BC2543 BC2543 ABC transporter ATP-binding protein (NCBI ptt file) 25, 245
BC2551 BC2551 Transcriptional activator tenA (NCBI ptt file) 25, 238
BC2587 BC2587 Phage Prohead Protease (NCBI ptt file) 25, 104
BC2590 BC2590 Phage protein (NCBI ptt file) 25, 131
BC2593 BC2593 Phage protein (NCBI ptt file) 25, 141
BC2691 BC2691 Acetyltransferase (NCBI ptt file) 25, 449
BC2709 BC2709 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 163, 279
BC2906 BC2906 hypothetical protein (NCBI ptt file) 25, 238
BC2986 BC2986 Alkaline phosphatase (NCBI ptt file) 25, 158
BC3020 BC3020 hypothetical protein (NCBI ptt file) 163, 258
BC3188 BC3188 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 163, 209
BC3198 BC3198 hypothetical protein (NCBI ptt file) 25, 487
BC3340 BC3340 tryptophanyl-tRNA synthetase (RefSeq) 163, 412
BC3426 BC3426 RNA polymerase sigma-I factor (NCBI ptt file) 146, 163
BC3431 BC3431 Lysine exporter protein (NCBI ptt file) 98, 163
BC3504 BC3504 (S)-2-hydroxy-acid oxidase chain D (NCBI ptt file) 154, 163
BC3515 BC3515 hypothetical Glycosyltransferase (NCBI ptt file) 25, 96
BC3518 BC3518 Response regulator aspartate phosphatase (NCBI ptt file) 20, 163
BC3589 BC3589 RNA polymerase ECF-type sigma factor (NCBI ptt file) 25, 163
BC3620 BC3620 Spore coat protein L (NCBI ptt file) 25, 46
BC3676 BC3676 hypothetical protein (NCBI ptt file) 163, 308
BC3724 BC3724 GABA-specific permease (NCBI ptt file) 146, 163
BC3879 BC3879 Transporter (NCBI ptt file) 25, 415
BC3984 BC3984 hypothetical protein (NCBI ptt file) 163, 316
BC3997 BC3997 Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) 25, 84
BC4044 BC4044 Sensory box/GGDEF family protein (NCBI ptt file) 25, 397
BC4075 BC4075 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 25, 162
BC4169 BC4169 hypothetical protein (NCBI ptt file) 146, 163
BC4228 BC4228 hypothetical protein (NCBI ptt file) 25, 128
BC4357 BC4357 (R)-specific enoyl-CoA hydratase (NCBI ptt file) 163, 525
BC4432 BC4432 Two-component sensor kinase yvcQ (NCBI ptt file) 163, 385
BC4527 BC4527 hypothetical Membrane Spanning Protein (NCBI ptt file) 25, 131
BC4539 BC4539 Two-component response regulator ycbL (NCBI ptt file) 163, 316
BC5030 BC5030 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 25, 415
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 BC3589
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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