Organism : Bacillus cereus ATCC14579 | Module List :
BC5193

COMF operon protein 1 (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) cog/ cog
nucleic acid binding go/ molecular_function
DNA binding go/ molecular_function
ATP binding go/ molecular_function
ATP-dependent helicase activity go/ molecular_function
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5193
(Mouseover regulator name to see its description)

BC5193 is regulated by 23 influences and regulates 0 modules.
Regulators for BC5193 (23)
Regulator Module Operator
BC0114 257 tf
BC0607 257 tf
BC0854 257 tf
BC1363 257 tf
BC1427 257 tf
BC1841 257 tf
BC1987 257 tf
BC2401 257 tf
BC2514 257 tf
BC3207 257 tf
BC3826 257 tf
BC4010 257 tf
BC5143 257 tf
BC0122 67 tf
BC0518 67 tf
BC1841 67 tf
BC2434 67 tf
BC2672 67 tf
BC3813 67 tf
BC3814 67 tf
BC3891 67 tf
BC4072 67 tf
BC4652 67 tf

Warning: BC5193 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
4054 2.10e+00 gacgGagG
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4055 1.80e+04 CGCAAGCc
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4430 5.50e+00 AAgGAGg
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4431 1.10e+04 gAtgAAGAGGaGC
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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 BC5193

BC5193 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) cog/ cog
nucleic acid binding go/ molecular_function
DNA binding go/ molecular_function
ATP binding go/ molecular_function
ATP-dependent helicase activity go/ molecular_function
zinc ion binding go/ molecular_function
Module neighborhood information for BC5193

BC5193 has total of 46 gene neighbors in modules 67, 257
Gene neighbors (46)
Gene Common Name Description Module membership
BC0014 BC0014 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 257, 461
BC0235 BC0235 hypothetical protein (NCBI ptt file) 67, 75
BC0564 BC0564 hypothetical lipoprotein (NCBI ptt file) 245, 257
BC0579 BC0579 Malate-sodium symport (NCBI ptt file) 234, 257
BC0674 BC0674 Permease (NCBI ptt file) 257, 465
BC0676 BC0676 hypothetical protein (NCBI ptt file) 257, 308
BC0803 BC0803 Sodium-dependent phosphate transporter (NCBI ptt file) 257, 388
BC0826 BC0826 hypothetical DNA-binding protein (NCBI ptt file) 141, 257
BC0855 BC0855 Multidrug resistance protein B (NCBI ptt file) 67, 161
BC0879 BC0879 hypothetical Membrane Associated Protein (NCBI ptt file) 257, 449
BC0941 BC0941 Type II restriction-modification system methylation subunit (NCBI ptt file) 257, 343
BC0942 BC0942 hypothetical protein (NCBI ptt file) 67, 351
BC1319 BC1319 Oxidoreductase (NCBI ptt file) 257, 449
BC1427 BC1427 CbiX protein (NCBI ptt file) 165, 257
BC1579 BC1579 putative synthetase/amidase (NCBI ptt file) 67, 256
BC1580 BC1580 surface protein (NCBI ptt file) 67, 256
BC1617 BC1617 hypothetical Cytosolic Protein (NCBI ptt file) 257, 443
BC1709 BC1709 malate-2H+/lactate-NA+ antiporter (NCBI ptt file) 67, 204
BC1759 BC1759 Tetracycline resistance protein (NCBI ptt file) 67, 492
BC2163 BC2163 TPR-repeat-containing protein (NCBI ptt file) 67, 288
BC2374 BC2374 hypothetical Membrane Spanning Protein (NCBI ptt file) 257, 281
BC2554 BC2554 hypothetical protein (NCBI ptt file) 257, 432
BC2894 BC2894 Macrolide-efflux protein (NCBI ptt file) 257, 343
BC3428 BC3428 Lysine exporter protein (NCBI ptt file) 256, 257
BC3524 BC3524 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 67, 139
BC3775 BC3775 Microsomal dipeptidase (NCBI ptt file) 257, 312
BC3810 BC3810 hypothetical Cytosolic Protein (NCBI ptt file) 67, 71
BC3811 BC3811 Bacterial Protein Translation Initiation Factor 2 (IF-2) (NCBI ptt file) 67, 462
BC3820 BC3820 Phosphatidate cytidylyltransferase (NCBI ptt file) 67, 182
BC4088 BC4088 IG hypothetical 17224 (NCBI ptt file) 257, 414
BC4275 BC4275 hypothetical protein (NCBI ptt file) 257, 461
BC4295 BC4295 DNA repair protein recO (NCBI ptt file) 252, 257
BC4299 BC4299 Diacylglycerol kinase (NCBI ptt file) 60, 67
BC4493 BC4493 Nucleoside-triphosphatase (NCBI ptt file) 67, 157
BC4511 BC4511 Acid phosphatase (NCBI ptt file) 221, 257
BC4688 BC4688 hypothetical protein (NCBI ptt file) 257, 313
BC4761 BC4761 S-adenosylmethionine synthetase (NCBI ptt file) 134, 257
BC4765 BC4765 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 67, 162
BC5026 BC5026 hypothetical protein (NCBI ptt file) 67, 432
BC5027 BC5027 Protein erfK/srfK precursor (NCBI ptt file) 67, 432
BC5192 BC5192 Competence protein F (NCBI ptt file) 60, 67
BC5193 BC5193 COMF operon protein 1 (NCBI ptt file) 67, 257
BC5238 BC5238 Glycine betaine transporter (NCBI ptt file) 67, 75
BC5370 BC5370 Agmatinase (NCBI ptt file) 257, 382
BC5407 BC5407 Chloride channel protein (NCBI ptt file) 67, 432
BC5420 BC5420 Glycosyltransferase (NCBI ptt file) 67, 75
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 BC5193
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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