Organism : Bacillus cereus ATCC14579 | Module List :
BC4236

ComG operon protein 4 (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Type II secretory pathway, pseudopilin PulG cog/ cog
IV_pilin_GFxxxE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4236
(Mouseover regulator name to see its description)

BC4236 is regulated by 29 influences and regulates 0 modules.
Regulators for BC4236 (29)
Regulator Module Operator
BC0042 321 tf
BC0613 321 tf
BC0848 321 tf
BC0958 321 tf
BC1059 321 tf
BC1731 321 tf
BC1884 321 tf
BC2250 321 tf
BC2386 321 tf
BC2444 321 tf
BC2517 321 tf
BC2837 321 tf
BC2903 321 tf
BC3320 321 tf
BC3690 321 tf
BC4240 321 tf
BC4395 321 tf
BC5176 321 tf
BC5363 321 tf
BC1059 263 tf
BC1489 263 tf
BC1531 263 tf
BC1987 263 tf
BC2351 263 tf
BC2401 263 tf
BC2794 263 tf
BC3497 263 tf
BC4930 263 tf
BC5340 263 tf

Warning: BC4236 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
4442 8.90e+02 aGGaggGAA
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4443 2.20e+03 ATTtCGcCG.aTgAtTCccc
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4556 1.50e-02 gtGggGAatga
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4557 3.90e+03 GCAAACTTCAAATTCCTATGTCG
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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 BC4236

BC4236 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Type II secretory pathway, pseudopilin PulG cog/ cog
IV_pilin_GFxxxE tigr/ tigrfam
Module neighborhood information for BC4236

BC4236 has total of 57 gene neighbors in modules 263, 321
Gene neighbors (57)
Gene Common Name Description Module membership
BC0035 BC0035 Arginine decarboxylase (NCBI ptt file) 263, 308
BC0189 BC0189 hypothetical protein (NCBI ptt file) 175, 263
BC0254 BC0254 Homogentisate 1,2-dioxygenase (NCBI ptt file) 243, 263
BC0312 BC0312 UDP-glucose 4-epimerase (NCBI ptt file) 9, 263
BC0391 BC0391 hypothetical protein (NCBI ptt file) 263, 351
BC0602 BC0602 Bacillolysin (NCBI ptt file) 104, 321
BC0664 BC0664 None 224, 263
BC0876 BC0876 hypothetical protein (NCBI ptt file) 86, 263
BC0948 BC0948 hypothetical protein (NCBI ptt file) 24, 321
BC1050 BC1050 ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) 263, 416
BC1132 BC1132 hypothetical protein (NCBI ptt file) 141, 263
BC1140 BC1140 Spore germination protein PF (NCBI ptt file) 263, 288
BC1144 BC1144 Spore germination protein PB (NCBI ptt file) 56, 263
BC1145 BC1145 Spore germination protein PA (NCBI ptt file) 26, 263
BC1176 BC1176 hypothetical protein (NCBI ptt file) 263, 284
BC1478 BC1478 Sensor protein resE (NCBI ptt file) 193, 263
BC1556 BC1556 hypothetical protein (NCBI ptt file) 263, 343
BC1772 BC1772 Beta-lactamase inhibitory protein II (NCBI ptt file) 26, 263
BC1895 BC1895 Phage protein (NCBI ptt file) 186, 321
BC2037 BC2037 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 329
BC2167 BC2167 Bacillolysin (NCBI ptt file) 321, 393
BC2275 BC2275 hypothetical cytosolic protein pX02-70 (NCBI ptt file) 263, 457
BC2351 BC2351 Transcriptional regulator, MerR family (NCBI ptt file) 263, 449
BC2395 BC2395 hypothetical protein (NCBI ptt file) 218, 321
BC2476 BC2476 phosphoesterase (NCBI ptt file) 263, 449
BC2507 BC2507 Transcriptional regulator, AraC family (NCBI ptt file) 225, 263
BC2604 BC2604 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 389
BC2673 BC2673 Tetracycline resistance determinant tetV (NCBI ptt file) 263, 465
BC2687 BC2687 hypothetical protein (NCBI ptt file) 127, 263
BC2810 BC2810 hypothetical protein (NCBI ptt file) 321, 453
BC3112 BC3112 None 232, 321
BC3192 BC3192 Protein ydhR precursor (NCBI ptt file) 179, 321
BC3560 BC3560 hypothetical Membrane Spanning Protein (NCBI ptt file) 222, 263
BC3622 BC3622 Multidrug resistance protein B (NCBI ptt file) 263, 468
BC3720 BC3720 Fructose repressor (NCBI ptt file) 234, 263
BC3897 BC3897 RNA binding protein (NCBI ptt file) 263, 281
BC4066 BC4066 Stage V sporulation protein AE (NCBI ptt file) 321, 355
BC4071 BC4071 Sodium/proline symporter (NCBI ptt file) 321, 405
BC4190 BC4190 Stage III sporulation protein AD (NCBI ptt file) 130, 321
BC4236 BC4236 ComG operon protein 4 (NCBI ptt file) 263, 321
BC4237 BC4237 ComG operon protein 3 (NCBI ptt file) 205, 321
BC4416 BC4416 Ferrichrome-binding protein (NCBI ptt file) 263, 449
BC4572 BC4572 hypothetical Cytosolic Protein (NCBI ptt file) 263, 455
BC4809 BC4809 Two component system histidine kinase (NCBI ptt file) 263, 449
BC4810 BC4810 Two-component response regulator (NCBI ptt file) 242, 263
BC4819 BC4819 hypothetical protein (NCBI ptt file) 263, 414
BC5216 BC5216 PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) 127, 263
BC5283 BC5283 Stage II sporulation protein Q (NCBI ptt file) 13, 321
BC5291 BC5291 NADH-quinone oxidoreductase chain N (NCBI ptt file) 321, 490
BC5294 BC5294 NADH-quinone oxidoreductase chain K (NCBI ptt file) 321, 484
BC5295 BC5295 NADH-quinone oxidoreductase chain J (NCBI ptt file) 321, 490
BC5296 BC5296 NADH-quinone oxidoreductase chain I (NCBI ptt file) 321, 393
BC5300 BC5300 NADH-quinone oxidoreductase chain B (NCBI ptt file) 321, 490
BC5301 BC5301 NADH-quinone oxidoreductase chain A (NCBI ptt file) 321, 490
BC5302 BC5302 Sensory box/GGDEF family protein (NCBI ptt file) 139, 321
BC5327 BC5327 Stage II sporulation protein R (NCBI ptt file) 108, 321
BC5448 BC5448 UDP-glucose 4-epimerase (NCBI ptt file) 146, 263
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 BC4236
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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