Organism : Campylobacter jejuni | Module List :
Cj0003 gyrB

DNA gyrase subunit B (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA modification go/ biological_process
gyrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0003
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0003!

Warning: Cj0003 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
7512 7.10e-01 TTtTcTCCTTgaTTT
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7513 1.60e+00 cTAAtAatAagcctatTGcaA..c
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7682 3.80e+03 CCAAGGAG
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7683 8.70e+03 Ct.TgAAAgtag
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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 Cj0003

Cj0003 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA modification go/ biological_process
gyrB tigr/ tigrfam
Module neighborhood information for Cj0003

Cj0003 has total of 39 gene neighbors in modules 65, 150
Gene neighbors (39)
Gene Common Name Description Module membership
Cj0002 dnaN DNA polymerase III, beta chain (NCBI ptt file) 65, 74
Cj0003 gyrB DNA gyrase subunit B (NCBI ptt file) 65, 150
Cj0057 Cj0057 putative periplasmic protein (NCBI ptt file) 3, 65
Cj0089 Cj0089 putative lipoprotein (NCBI ptt file) 18, 65
Cj0090 Cj0090 putative lipoprotein (NCBI ptt file) 57, 65
Cj0091 Cj0091 putative lipoprotein (NCBI ptt file) 65, 90
Cj0100 Cj0100 parA family protein (NCBI ptt file) 65, 128
Cj0109 exbB3 exbB olQ family transport protein (VIMSS-AUTO) 150, 151
Cj0110 exbD3 exbD 150, 151
Cj0111 Cj0111 periplasmic protein (NCBI ptt file) 150, 151
Cj0112 Cj0112 periplasmic protein (NCBI ptt file) 150, 151
Cj0116 fabD malonyl CoA-acyl carrier protein transacylase (NCBI ptt file) 150, 151
Cj0118 Cj0118 hypothetical protein Cj0118 (NCBI ptt file) 150, 151
Cj0119 Cj0119 hypothetical protein Cj0119 (NCBI ptt file) 150, 151
Cj0120 Cj0120 hypothetical protein Cj0120 (NCBI ptt file) 88, 150
Cj0121 Cj0121 hypothetical protein Cj0121 (NCBI ptt file) 150, 151
Cj0130 tyrA putative prephenate dehydrogenase (NCBI ptt file) 65, 90
Cj0206 thrS threonyl-tRNA synthetase (NCBI ptt file) 65, 151
Cj0232c Cj0232c putative integral membrane protein (NCBI ptt file) 83, 150
Cj0258 Cj0258 putative helix-turn-helix motif protein (NCBI ptt file) 76, 150
Cj0302c Cj0302c hypothetical protein Cj0302c (NCBI ptt file) 6, 150
Cj0524 Cj0524 hypothetical protein Cj0524 (NCBI ptt file) 1, 150
Cj0564 Cj0564 putative integral membrane protein (NCBI ptt file) 117, 150
Cj0826 Cj0826 putative integral membrane protein (NCBI ptt file) 104, 150
Cj0859c Cj0859c hypothetical protein Cj0859c (NCBI ptt file) 65, 78
Cj0860 Cj0860 probable integral membrane protein (NCBI ptt file) 65, 69
Cj0980 Cj0980 putative peptidase (NCBI ptt file) 65, 111
Cj0983 Cj0983 putative lipoprotein (NCBI ptt file) 117, 150
Cj1082c thiD phosphomethylpyrimidine kinase (NCBI ptt file) 65, 118
Cj1083c Cj1083c possible nuclease (NCBI ptt file) 65, 150
Cj1084c Cj1084c putative ATP/GTP-binding protein (NCBI ptt file) 56, 65
Cj1090c Cj1090c putative lipoprotein (NCBI ptt file) 65, 118
Cj1114c pssA CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 60, 150
Cj1115c Cj1115c putative membrane protein (NCBI ptt file) 52, 150
Cj1317 neuB3 N-acetylneuraminic acid synthetase (NCBI ptt file) 65, 127
Cj1435c Cj1435c hypothetical protein Cj1435c (NCBI ptt file) 60, 150
Cj1677 Cj1677 putative lipoprotein (NCBI) 81, 150
VIMSS45983 VIMSS45983 None 28, 150
VIMSS46848 VIMSS46848 None 2, 150
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 Cj0003
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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