Organism : Bacillus cereus ATCC14579 | Module List :
BC0242

Oligopeptide transport system permease protein oppB (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0242
(Mouseover regulator name to see its description)

BC0242 is regulated by 23 influences and regulates 0 modules.
Regulators for BC0242 (23)
Regulator Module Operator
BC0405 514 tf
BC0742 514 tf
BC0840 514 tf
BC1427 514 tf
BC1851 514 tf
BC2401 514 tf
BC3320 514 tf
BC4076 514 tf
BC5352 514 tf
BC5385 514 tf
BC0405 332 tf
BC0742 332 tf
BC0758 332 tf
BC0840 332 tf
BC1033 332 tf
BC1427 332 tf
BC1490 332 tf
BC1622 332 tf
BC1851 332 tf
BC2401 332 tf
BC3653 332 tf
BC4076 332 tf
BC4222 332 tf

Warning: BC0242 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
4576 2.80e-12 GCtgATtgGAaAAaccaaAGG
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4577 1.10e-01 cAGGGG
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4938 2.50e-08 GCtaATcgGAaAAaccaaAGGca
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4939 1.50e-01 cAGGGG.A
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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 BC0242

BC0242 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for BC0242

BC0242 has total of 23 gene neighbors in modules 332, 514
Gene neighbors (23)
Gene Common Name Description Module membership
BC0241 BC0241 Oligopeptide-binding protein oppA (NCBI ptt file) 332, 514
BC0242 BC0242 Oligopeptide transport system permease protein oppB (NCBI ptt file) 332, 514
BC0243 BC0243 Oligopeptide transport system permease protein oppC (NCBI ptt file) 332, 514
BC0244 BC0244 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 332, 514
BC0245 BC0245 Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) 332, 514
BC0907 BC0907 Oligopeptide-binding protein oppA (NCBI ptt file) 332, 514
BC0908 BC0908 Oligopeptide transport system permease protein oppB (NCBI ptt file) 332, 514
BC0909 BC0909 Oligopeptide transport system permease protein oppC (NCBI ptt file) 332, 514
BC0910 BC0910 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 332, 514
BC0911 BC0911 Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) 332, 514
BC1090 BC1090 Sulfate-binding protein (NCBI ptt file) 332, 514
BC1093 BC1093 Sulfate transport system permease protein cysW (NCBI ptt file) 332, 514
BC1421 BC1421 Phosphoadenosine phosphosulfate reductase (NCBI ptt file) 332, 514
BC1422 BC1422 Sulfate adenylyltransferase (NCBI ptt file) 332, 514
BC1423 BC1423 Adenylylsulfate kinase (NCBI ptt file) 332, 514
BC1424 BC1424 Ferredoxin--nitrite reductase (NCBI ptt file) 332, 514
BC1425 BC1425 hypothetical protein (NCBI ptt file) 332, 514
BC1426 BC1426 Uroporphyrin-III C-methyltransferase (NCBI ptt file) 338, 514
BC2910 BC2910 Alkanesulfonates transport system permease protein (NCBI ptt file) 332, 514
BC2911 BC2911 Alkanesulfonates-binding protein (NCBI ptt file) 332, 514
BC2912 BC2912 Alkanesulfonates transport ATP-binding protein (NCBI ptt file) 332, 514
BC3047 BC3047 Serine/threonine protein phosphatase (NCBI ptt file) 254, 332
BC3050 BC3050 hypothetical Membrane Spanning Protein (NCBI ptt file) 332, 514
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 BC0242
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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