Organism : Bacillus cereus ATCC14579 | Module List :
BC3904

RNA polymerase sigma-E 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_sigmaE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3904
(Mouseover regulator name to see its description)

BC3904 is regulated by 21 influences and regulates 37 modules.
Regulators for BC3904 (21)
Regulator Module Operator
BC0742 101 tf
BC1059 101 tf
BC1080 101 tf
BC1115 101 tf
BC1329 101 tf
BC2178 101 tf
BC2469 101 tf
BC2517 101 tf
BC2811 101 tf
BC3588 101 tf
BC3904 101 tf
BC4336 101 tf
BC1059 508 tf
BC1329 508 tf
BC1363 508 tf
BC2401 508 tf
BC2410 508 tf
BC2469 508 tf
BC2517 508 tf
BC2964 508 tf
BC3904 508 tf

Warning: BC3904 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
4118 4.40e+00 AatgAggGgaG
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4119 2.50e+03 GGCGCAC
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4926 3.50e-01 aaGAGgggAA
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4927 4.50e+01 TTgcggAggtGTcTTTTTAT
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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 BC3904

BC3904 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_sigmaE tigr/ tigrfam
Module neighborhood information for BC3904

BC3904 has total of 24 gene neighbors in modules 101, 508
Gene neighbors (24)
Gene Common Name Description Module membership
BC0787 BC0787 Stage V sporulation protein R (NCBI ptt file) 344, 508
BC0935 BC0935 Citrate-proton symporter (NCBI ptt file) 144, 508
BC1092 BC1092 Sulfate transport system permease protein cysT (NCBI ptt file) 101, 349
BC1115 BC1115 Transcriptional regulator, AraC family (NCBI ptt file) 68, 101
BC1192 BC1192 putative competence protein/transcription factor (NCBI ptt file) 497, 508
BC1228 BC1228 hypothetical protein (NCBI ptt file) 101, 526
BC1428 BC1428 Ferrochelatase (NCBI ptt file) 101, 349
BC1621 BC1621 Macrolide-efflux protein (NCBI ptt file) 323, 508
BC1868 BC1868 Phage protein (NCBI ptt file) 195, 508
BC2050 BC2050 Stage II sporulation protein P (NCBI ptt file) 101, 210
BC2177 BC2177 Aspartate racemase (NCBI ptt file) 101, 156
BC2187 BC2187 Phosphoglycolate phosphatase (NCBI ptt file) 68, 101
BC2624 BC2624 Integral membrane protein (NCBI ptt file) 278, 508
BC2650 BC2650 TerF-related protein (NCBI ptt file) 111, 508
BC2780 BC2780 hypothetical protein (NCBI ptt file) 101, 472
BC2853 BC2853 D-threo-aldose 1-dehydrogenase (NCBI ptt file) 106, 508
BC2856 BC2856 Ankyrin repeat protein (NCBI ptt file) 373, 508
BC2905 BC2905 hypothetical protein (NCBI ptt file) 101, 472
BC2909 BC2909 Alkanesulfonate monooxygenase (NCBI ptt file) 101, 349
BC3009 BC3009 Microbial collagenase (NCBI ptt file) 323, 508
BC3441 BC3441 Lysozyme M1 precursor (NCBI ptt file) 101, 160
BC3566 BC3566 Molybdopterin biosynthesis MoeA protein (NCBI ptt file) 195, 508
BC3904 BC3904 RNA polymerase sigma-E factor (NCBI ptt file) 101, 508
BC4736 BC4736 VrrB (NCBI ptt file) 309, 508
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 BC3904
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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