Organism : Bacillus subtilis | Module List :
BSU16470 sigD

RNA polymerase sigma factor SigD (RefSeq)

CircVis
Functional Annotations (9)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase 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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16470
(Mouseover regulator name to see its description)

BSU16470 is regulated by 14 influences and regulates 20 modules.
Regulators for BSU16470 sigD (14)
Regulator Module Operator
BSU01430 2 tf
BSU16470 2 tf
BSU28410 2 tf
BSU01070 382 tf
BSU02370 382 tf
BSU04820 382 tf
BSU06700 382 tf
BSU16470 382 tf
BSU21700 382 tf
BSU21780 382 tf
BSU22120 382 tf
BSU25250 382 tf
BSU33580 382 tf
BSU37080 382 tf
Regulated by BSU16470 (20)
Module Residual Genes
2 0.23 20
45 0.33 18
57 0.22 16
60 0.41 4
75 0.32 23
81 0.43 5
118 0.22 17
119 0.36 19
128 0.54 29
135 0.33 23
165 0.43 7
175 0.36 22
179 0.54 8
209 0.23 15
235 0.46 20
254 0.34 23
355 0.29 14
366 0.22 13
382 0.30 20
383 0.20 16
Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
5676 5.10e+01 GAGGatGAaAAA
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5677 3.90e+03 AAAggGGaTTT
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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 BSU16470

BSU16470 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase 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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
Module neighborhood information for BSU16470

BSU16470 has total of 37 gene neighbors in modules 2, 382
Gene neighbors (37)
Gene Common Name Description Module membership
BSU02230 purT phosphoribosylglycinamide formyltransferase 2 (RefSeq) 135, 382
BSU06670 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C (RefSeq) 312, 382
BSU06680 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq) 312, 382
BSU16330 cheY regulator of chemotaxis and motility (RefSeq) 2, 254
BSU16340 fliZ flagella biosynthesis protein FliZ (RefSeq) 2, 382
BSU16350 fliP flagellar biosynthesis protein FliP (RefSeq) 2, 254
BSU16360 fliQ flagellar biosynthesis protein FliQ (RefSeq) 2, 45
BSU16370 fliR flagellar biosynthesis protein FliR (RefSeq) 2, 382
BSU16380 flhB flagellar biosynthesis protein FlhB (RefSeq) 2, 45
BSU16390 flhA flagellar biosynthesis protein FlhA (RefSeq) 2, 45
BSU16400 flhF flagellar biosynthesis regulator FlhF (RefSeq) 2, 45
BSU16410 ylxH essential component of the flagellar assembly machinery (RefSeq) 2, 45
BSU16420 cheB chemotaxis-specific methylesterase (RefSeq) 2, 45
BSU16430 cheA chemotactic two-component sensor histidine kinase (RefSeq) 2, 45
BSU16440 cheW modulation of CheA activity in response to attractants (chemotaxis) (RefSeq) 2, 45
BSU16450 cheC signal terminating phosphatase of CheR-mediated methylation of methyl-accepting chemotaxis proteins (MCPs) (RefSeq) 2, 235
BSU16460 cheD sequence specific deamidase required for methylation of methyl-accepting chemotaxis proteins (MCPs) by CheR (RefSeq) 2, 45
BSU16470 sigD RNA polymerase sigma factor SigD (RefSeq) 2, 382
BSU16480 ylxL coupling factor for flagellin transcription and translation (RefSeq) 2, 254
BSU22190 ypsA hypothetical protein (RefSeq) 382, 385
BSU22370 aspB aspartate aminotransferase (RefSeq) 382, 385
BSU22380 ypmB hypothetical protein (RefSeq) 382, 385
BSU22390 ypmA hypothetical protein (RefSeq) 382, 385
BSU22410 panD aspartate alpha-decarboxylase (RefSeq) 227, 382
BSU22420 panC pantoate--beta-alanine ligase (RefSeq) 227, 382
BSU22430 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (RefSeq) 227, 382
BSU22440 birA biotin acetyl-CoA-carboxylase ligase and biotin regulon repressor (RefSeq) 382, 385
BSU22450 cca tRNA CCA-pyrophosphorylase (RefSeq) 312, 382
BSU22460 ypjH putative enzyme in leucine catabolism or biotin metabolism (RefSeq) 187, 382
BSU22470 ypjG hypothetical protein (RefSeq) 187, 382
BSU22480 mgsA methylglyoxal synthase (RefSeq) 312, 382
BSU22490 dapB dihydrodipicolinate reductase (RefSeq) 312, 382
BSU22500 ypjD nucleotide phosphohydrolase (RefSeq) 312, 382
BSU35620 lytC N-acetylmuramoyl-L-alanine amidase (major autolysin) (RefSeq) 2, 254
BSU35630 lytB modifier protein of major autolysin LytC (RefSeq) 2, 254
VIMSS39609 VIMSS39609 None 2, 29
VIMSS39965 VIMSS39965 None 2, 235
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 BSU16470
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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