Organism : Bacillus cereus ATCC14579 | Module List :
BC2794

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 BC2794
(Mouseover regulator name to see its description)

BC2794 is regulated by 26 influences and regulates 31 modules.
Regulators for BC2794 (26)
Regulator Module Operator
BC0649 63 tf
BC0758 63 tf
BC0950 63 tf
BC2444 63 tf
BC2794 63 tf
BC3160 63 tf
BC3244 63 tf
BC3493 63 tf
BC3497 63 tf
BC0586 105 tf
BC0954 105 tf
BC1296 105 tf
BC1489 105 tf
BC1490 105 tf
BC1531 105 tf
BC2794 105 tf
BC3706 105 tf
BC3922 105 tf
BC4081 105 tf
BC4174 105 tf
BC4211 105 tf
BC4832 105 tf
BC4834 105 tf
BC4968 105 tf
BC5205 105 tf
BC5265 105 tf

Warning: BC2794 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
4046 1.20e+04 GaGgaggA
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4047 1.90e+04 CAGCGCCc
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4126 6.30e-01 CCtCCTttatt
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4127 1.40e+04 gtGggAAGCG
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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 BC2794

BC2794 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 BC2794

BC2794 has total of 62 gene neighbors in modules 63, 105
Gene neighbors (62)
Gene Common Name Description Module membership
BC0013 BC0013 Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) 63, 137
BC0476 BC0476 Acetylornithine deacetylase (NCBI ptt file) 105, 491
BC0565 BC0565 Ankyrin (NCBI ptt file) 63, 265
BC0572 BC0572 Two-component response regulator (NCBI ptt file) 63, 286
BC0597 BC0597 Nicotinate phosphoribosyltransferase (NCBI ptt file) 105, 287
BC0649 BC0649 Transcriptional regulator, DeoR family (NCBI ptt file) 63, 246
BC0766 BC0766 Methylthioribose transport system permease protein (NCBI ptt file) 20, 63
BC1097 BC1097 hypothetical protein (NCBI ptt file) 63, 286
BC1111 BC1111 phosphoesterase (NCBI ptt file) 105, 491
BC1258 BC1258 hypothetical protein (NCBI ptt file) 63, 427
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1912 BC1912 Phage protein (NCBI ptt file) 63, 137
BC1913 BC1913 Phage protein (NCBI ptt file) 63, 137
BC1914 BC1914 Phage protein (NCBI ptt file) 63, 146
BC1923 BC1923 hypothetical Membrane Spanning Protein (NCBI ptt file) 57, 105
BC2232 BC2232 Glycine betaine transport ATP-binding protein (NCBI ptt file) 105, 116
BC2233 BC2233 Glycine betaine transport system permease protein / Glycine betaine-binding protein (NCBI ptt file) 105, 116
BC2315 BC2315 DinB protein (NCBI ptt file) 63, 163
BC2428 BC2428 hypothetical protein (NCBI ptt file) 63, 225
BC2539 BC2539 Two-component sensor kinase yxdK (NCBI ptt file) 6, 63
BC2603 BC2603 hypothetical protein (NCBI ptt file) 63, 299
BC2740 BC2740 Protein translocase subunit SecY (NCBI ptt file) 6, 63
BC2793 BC2793 ATP-dependent Clp protease proteolytic subunit (NCBI ptt file) 105, 491
BC2794 BC2794 RNA polymerase ECF-type sigma factor (NCBI ptt file) 63, 105
BC3045 BC3045 hypothetical Membrane Spanning Protein (NCBI ptt file) 105, 237
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3369 BC3369 Gluconokinase (NCBI ptt file) 105, 116
BC3370 BC3370 Gluconate permease (NCBI ptt file) 105, 116
BC3371 BC3371 Transaldolase (NCBI ptt file) 105, 116
BC3373 BC3373 None 105, 116
BC3416 BC3416 SMS protein (NCBI ptt file) 105, 258
BC3497 BC3497 Transcriptional regulator, ArsR family (NCBI ptt file) 63, 146
BC3498 BC3498 Quinone oxidoreductase (NCBI ptt file) 63, 465
BC3584 BC3584 Oligopeptide-binding protein oppA (NCBI ptt file) 55, 63
BC3645 BC3645 CcdC protein (NCBI ptt file) 63, 285
BC3673 BC3673 hypothetical Membrane Spanning Protein (NCBI ptt file) 105, 116
BC3747 BC3747 Sensory box/GGDEF family protein (NCBI ptt file) 63, 286
BC3786 BC3786 Zinc protease (NCBI ptt file) 105, 288
BC3787 BC3787 Zinc protease (NCBI ptt file) 105, 258
BC3876 BC3876 hypothetical protein (NCBI ptt file) 63, 228
BC4014 BC4014 Neopullulanase (NCBI ptt file) 63, 299
BC4131 BC4131 hypothetical protein (NCBI ptt file) 63, 299
BC4146 BC4146 Protein erfK/srfK precursor (NCBI ptt file) 20, 63
BC4147 BC4147 Integral membrane protein (NCBI ptt file) 63, 482
BC4305 BC4305 hypothetical Cytosolic Protein (NCBI ptt file) 63, 72
BC4464 BC4464 Folylpolyglutamate synthase (NCBI ptt file) 48, 63
BC4502 BC4502 Xanthine permease (NCBI ptt file) 105, 254
BC4503 BC4503 Cytosine deaminase (NCBI ptt file) 105, 116
BC4514 BC4514 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 63, 288
BC4624 fabG 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq) 105, 116
BC4666 BC4666 Two component system histidine kinase (NCBI ptt file) 63, 308
BC4839 BC4839 ABC transporter ATP-binding protein (NCBI ptt file) 63, 453
BC4915 BC4915 ComA operon protein 2 (NCBI ptt file) 105, 491
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
BC4947 BC4947 hypothetical protein (NCBI ptt file) 20, 63
BC4977 BC4977 5'-nucleotidase (NCBI ptt file) 105, 445
BC5068 BC5068 CrcB family protein (NCBI ptt file) 63, 285
BC5319 BC5319 Protein tyrosine phosphatase (NCBI ptt file) 105, 116
BC5398 BC5398 Uracil-DNA glycosylase (NCBI ptt file) 105, 237
BC5401 BC5401 Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) 105, 287
VIMSS12791521 VIMSS12791521 None 105, 116
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 BC2794
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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