Organism : Campylobacter jejuni | Module List :
Cj0082 cydB

cytochrome bd oxidase subunit II (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Cytochrome bd-type quinol oxidase, subunit 2 cog/ cog
electron transport go/ biological_process
membrane go/ cellular_component
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cydB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0082
(Mouseover regulator name to see its description)

Cj0082 is regulated by 3 influences and regulates 0 modules.
Regulators for Cj0082 cydB (3)
Regulator Module Operator
Cj0101 128 tf
Cj0473 128 tf
Cj1533c 128 tf

Warning: Cj0082 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
7470 1.10e+00 TataAAgaTaTTTAAgc.aAAA
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7471 1.20e-02 caaAAaTTTccTTatAAttTctcG
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7638 2.90e+02 GCaaGtGG
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7639 6.70e+03 TcCCCC
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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 Cj0082

Cj0082 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Cytochrome bd-type quinol oxidase, subunit 2 cog/ cog
electron transport go/ biological_process
membrane go/ cellular_component
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
cydB tigr/ tigrfam
Module neighborhood information for Cj0082

Cj0082 has total of 51 gene neighbors in modules 44, 128
Gene neighbors (51)
Gene Common Name Description Module membership
Cj0030 Cj0030 hypothetical protein Cj0030 (NCBI ptt file) 58, 128
Cj0078c cdtB cytolethal distending toxin (NCBI ptt file) 44, 95
Cj0079c cdtA cytolethal distending toxin (NCBI ptt file) 44, 95
Cj0080 Cj0080 putative membrane protein (NCBI ptt file) 44, 60
Cj0081 cydA cytochrome bd oxidase subunit I (NCBI ptt file) 44, 151
Cj0082 cydB cytochrome bd oxidase subunit II (NCBI ptt file) 44, 128
Cj0098 fmt methionyl-tRNA formyltransferase (NCBI ptt file) 58, 128
Cj0100 Cj0100 parA family protein (NCBI ptt file) 65, 128
Cj0101 Cj0101 parB family protein (NCBI ptt file) 26, 128
Cj0263 Cj0263 putative integral membrane protein (NCBI ptt file) 66, 128
Cj0334 ahpC alkyl hydroperoxide reductase (NCBI ptt file) 16, 128
Cj0336c motB putative flagellar motor protein (NCBI ptt file) 44, 123
Cj0338c polA DNA polymerase I (NCBI ptt file) 39, 44
Cj0339 Cj0339 putative transmembrane transport protein (NCBI ptt file) 44, 78
Cj0504c Cj0504c hypothetical protein Cj0504c (NCBI ptt file) 48, 128
Cj0644 Cj0644 hypothetical protein Cj0644 (NCBI ptt file) 44, 165
Cj0763c cysE serine acetyltransferase (NCBI ptt file) 44, 45
Cj0877c Cj0877c very hypothetical protein Cj0877c (NCBI ptt file) 44, 58
Cj1000 Cj1000 putative transcriptional regulator (lysR family) (NCBI ptt file) 44, 63
Cj1013c Cj1013c putative membrane protein (NCBI ptt file) 128, 151
Cj1014c livF branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) 128, 151
Cj1016c livM putative branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) 104, 128
Cj1017c livH branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) 128, 151
Cj1019c livJ branched-chain amino-acid ABC transport system periplasmic binding protein (NCBI ptt file) 61, 128
Cj1033 Cj1033 putative integral membrane component of efflux system (NCBI ptt file) 117, 128
Cj1039 murG putative UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 44, 116
Cj1163c Cj1163c putative cation transport protein (NCBI ptt file) 51, 128
Cj1208 Cj1208 hypothetical protein Cj1208 (NCBI ptt file) 92, 128
Cj1375 Cj1375 putative efflux protein (NCBI ptt file) 128, 148
Cj1379 selB putative selenocysteine-specific elongation factor (NCBI ptt file) 44, 81
Cj1385 katA catalase (NCBI ptt file) 16, 128
Cj1434c Cj1434c putative sugar transferase (NCBI ptt file) 41, 44
Cj1440c Cj1440c putative sugar transferase (NCBI ptt file) 128, 141
Cj1458c thiL putative thiamin-monophosphate kinase (NCBI ptt file) 44, 63
Cj1459 Cj1459 hypothetical protein Cj1459 (NCBI ptt file) 44, 132
Cj1460 Cj1460 hypothetical protein Cj1460 (NCBI ptt file) 37, 44
Cj1461 Cj1461 possible DNA methylase (NCBI ptt file) 27, 44
Cj1479c rpsI 30S ribosomal protein S9 (NCBI ptt file) 111, 128
Cj1483c Cj1483c putative lipoprotein (NCBI ptt file) 26, 44
Cj1530 Cj1530 putative ATP/GTP-binding protein (NCBI ptt file) 44, 132
Cj1533c Cj1533c putative helix-turn-helix containsing protein (NCBI ptt file) 109, 128
Cj1544c Cj1544c putative integral membrane protein (NCBI ptt file) 41, 44
Cj1580c Cj1580c putative peptide ABC-transport system ATP-binding protein (NCBI ptt file) 56, 128
Cj1641 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diami ligase (NCBI ptt file) 18, 44
Cj1670c Cj1670c putative periplasmic protein (NCBI ptt file) 128, 141
Cj1687 Cj1687 putative efflux protein (NCBI ptt file) 44, 54
Cj1688c secY preprotein translocase subunit (NCBI ptt file) 128, 151
Cj1689c rplO 50S ribosomal protein L15 (NCBI ptt file) 128, 138
Cj1709c Cj1709c putative ribosomal pseudouridine synthase (NCBI ptt file) 128, 141
Cj1710c Cj1710c hypothetical protein Cj1710c (NCBI ptt file) 128, 151
Cj1711c ksgA putative dimethyladenosine transferase (16S rRNA dimethylase) (NCBI ptt file) 128, 151
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 Cj0082
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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