Organism : Bacillus cereus ATCC14579 | Module List :
BC4072

RNA polymerase sigma-F 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_sigF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4072
(Mouseover regulator name to see its description)

BC4072 is regulated by 21 influences and regulates 44 modules.
Regulators for BC4072 (21)
Regulator Module Operator
BC1080 420 tf
BC2250 420 tf
BC2770 420 tf
BC2971 420 tf
BC3826 420 tf
BC4072 420 tf
BC4525 420 tf
BC0123 203 tf
BC0473 203 tf
BC0953 203 tf
BC1037 203 tf
BC1915 203 tf
BC2386 203 tf
BC2672 203 tf
BC2738 203 tf
BC2794 203 tf
BC3244 203 tf
BC4072 203 tf
BC4073 203 tf
BC4652 203 tf
BC4902 203 tf

Warning: BC4072 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
4322 1.60e-07 aGgatTttaa.tat.TatataGAA
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4323 1.80e-01 AggGGAGga
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4750 1.60e-03 AGGgGG
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4751 3.80e+01 gtaGttgtgacgAtaAtTcgGcAT
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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 BC4072

BC4072 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_sigF tigr/ tigrfam
Module neighborhood information for BC4072

BC4072 has total of 40 gene neighbors in modules 203, 420
Gene neighbors (40)
Gene Common Name Description Module membership
BC1079 BC1079 hypothetical protein (NCBI ptt file) 203, 211
BC1241 BC1241 hypothetical protein (NCBI ptt file) 29, 420
BC1338 BC1338 Oligoendopeptidase F (NCBI ptt file) 203, 395
BC1368 BC1368 Nitropropane dioxygenase / Trans-enoyl-CoA reductase family (NCBI ptt file) 29, 420
BC1566 BC1566 Thermostable carboxypeptidase 1 (NCBI ptt file) 203, 299
BC1594 BC1594 Isochorismatase (NCBI ptt file) 203, 395
BC1701 BC1701 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 29, 420
BC1915 BC1915 Transcriptional regulator, PBSX family (NCBI ptt file) 203, 422
BC1947 BC1947 hypothetical protein (NCBI ptt file) 173, 420
BC2048 BC2048 Protein secretion chaperonin CsaA (NCBI ptt file) 29, 420
BC2049 BC2049 hypothetical protein (NCBI ptt file) 29, 420
BC2053 BC2053 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 409, 420
BC2182 BC2182 Histidinol-phosphatase (NCBI ptt file) 203, 395
BC2183 BC2183 Acetyltransferase (NCBI ptt file) 203, 395
BC2235 BC2235 hypothetical protein (NCBI ptt file) 203, 422
BC2250 BC2250 L-lysine aminomutase regulator (NCBI ptt file) 359, 420
BC2292 BC2292 3-hydroxyisobutyryl-coenzyme A hydrolase (NCBI ptt file) 173, 203
BC2500 BC2500 hypothetical protein (NCBI ptt file) 29, 420
BC2504 BC2504 Acetyltransferase (NCBI ptt file) 113, 420
BC2524 BC2524 Oligoendopeptidase F (NCBI ptt file) 173, 203
BC2534 BC2534 hypothetical Membrane Associated Protein (NCBI ptt file) 203, 211
BC2658 BC2658 Serine/threonine protein kinase (NCBI ptt file) 203, 409
BC2697 BC2697 Translation initiation inhibitor (NCBI ptt file) 203, 299
BC2737 BC2737 hypothetical protein (NCBI ptt file) 203, 299
BC2738 BC2738 Transcriptional regulator, AraC family (NCBI ptt file) 173, 203
BC2782 BC2782 Glutamate-rich protein grpB (NCBI ptt file) 203, 299
BC2971 BC2971 Transcriptional regulator, ArsR family (NCBI ptt file) 57, 420
BC2990 BC2990 Phosphoglycolate phosphatase (NCBI ptt file) 211, 420
BC2991 BC2991 Uridine kinase (NCBI ptt file) 258, 420
BC2992 BC2992 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 258, 420
BC2993 BC2993 Lactoylglutathione lyase (NCBI ptt file) 211, 420
BC3057 BC3057 Methyltransferase (NCBI ptt file) 173, 203
BC3133 BC3133 putative hydrolase (NCBI ptt file) 29, 420
BC3549 BC3549 Acetyltransferase (NCBI ptt file) 203, 211
BC3999 BC3999 hypothetical protein (NCBI ptt file) 29, 420
BC4072 BC4072 RNA polymerase sigma-F factor (NCBI ptt file) 203, 420
BC4073 BC4073 Anti-sigma F factor (NCBI ptt file) 203, 491
BC4074 BC4074 Anti-sigma F factor antagonist (NCBI ptt file) 203, 409
BC4613 BC4613 Metal-dependent hydrolase (NCBI ptt file) 203, 216
BC5019 BC5019 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 203, 211
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 BC4072
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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