Organism : Bacillus cereus ATCC14579 | Module List :
BC0208

Oligopeptide transport system permease protein oppC (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 BC0208
(Mouseover regulator name to see its description)

BC0208 is regulated by 34 influences and regulates 0 modules.
Regulators for BC0208 (34)
Regulator Module Operator
BC0498 53 tf
BC0607 53 tf
BC0848 53 tf
BC1427 53 tf
BC1490 53 tf
BC2181 53 tf
BC2979 53 tf
BC3128 53 tf
BC3320 53 tf
BC3493 53 tf
BC4057 53 tf
BC4076 53 tf
BC4474 53 tf
BC4650 53 tf
BC4826 53 tf
BC5000 53 tf
BC5411 53 tf
BC0607 318 tf
BC0848 318 tf
BC0856 318 tf
BC1427 318 tf
BC1732 318 tf
BC2351 318 tf
BC2401 318 tf
BC2979 318 tf
BC3128 318 tf
BC3155 318 tf
BC3190 318 tf
BC3405 318 tf
BC3493 318 tf
BC4076 318 tf
BC4474 318 tf
BC4826 318 tf
BC5143 318 tf

Warning: BC0208 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
4026 9.40e+01 GcACcAGCccc
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4027 2.80e+02 AACcCcc
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4550 1.10e-15 gacACGGTGCTAATTCcaGCAa
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4551 1.40e-04 tTGAaAGATAAGagggagg
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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 BC0208

BC0208 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 BC0208

BC0208 has total of 20 gene neighbors in modules 53, 318
Gene neighbors (20)
Gene Common Name Description Module membership
BC0207 BC0207 Oligopeptide transport system permease protein oppB (NCBI ptt file) 318, 408
BC0208 BC0208 Oligopeptide transport system permease protein oppC (NCBI ptt file) 53, 318
BC0209 BC0209 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 53, 318
BC0210 BC0210 Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) 53, 318
BC0211 BC0211 Oligopeptide-binding protein oppA (NCBI ptt file) 318, 408
BC0767 BC0767 Methylthioribose transport ATP-binding protein (NCBI ptt file) 318, 338
BC0768 BC0768 Methylthioribose-binding protein (NCBI ptt file) 318, 338
BC3176 BC3176 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 318, 408
BC4032 BC4032 Methylthioribose salvage protein (NCBI ptt file) 318, 338
BC4033 BC4033 5-methylthioribose kinase (NCBI ptt file) 318, 408
BC4036 BC4036 Ribulose bisphosphate carboxylase large chain (NCBI ptt file) 53, 215
BC4037 BC4037 Methylthioribose salvage protein (putative phosphatase) (NCBI ptt file) 53, 215
BC4038 BC4038 Methylthioribose salvage protein (putative aldolase) (NCBI ptt file) 53, 318
BC4039 BC4039 2-hydroxy-3-oxo-5-methylthiopent-2-enoate oxidase (NCBI ptt file) 53, 215
BC4250 BC4250 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file) 318, 338
BC4253 BC4253 Cystathionine gamma-synthase (NCBI ptt file) 215, 318
BC4984 BC4984 ABC transporter substrate-binding protein (NCBI ptt file) 53, 215
BC4985 BC4985 ABC transporter substrate-binding protein (NCBI ptt file) 53, 215
BC4986 BC4986 ABC transporter permease protein (NCBI ptt file) 53, 215
BC4987 BC4987 ABC transporter ATP-binding protein (NCBI ptt file) 53, 215
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 BC0208
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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