Organism : Campylobacter jejuni | Module List :
Cj1731c ruvC

crossover junction endodeoxyribonuclease (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Holliday junction resolvasome, endonuclease subunit cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
crossover junction endodeoxyribonuclease activity go/ molecular_function
lipoate-protein ligase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
ruvC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1731c
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj1731c!

Warning: Cj1731c 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
7652 3.30e+03 CTCaCACTC
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7653 5.20e+03 ATGGcG
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7690 1.60e+04 GATcTGCC
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7691 1.60e+04 CCaAAGG
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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 Cj1731c

Cj1731c is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Holliday junction resolvasome, endonuclease subunit cog/ cog
nucleic acid binding go/ molecular_function
DNA repair go/ biological_process
DNA recombination go/ biological_process
crossover junction endodeoxyribonuclease activity go/ molecular_function
lipoate-protein ligase activity go/ molecular_function
Homologous recombination kegg/ kegg pathway
ruvC tigr/ tigrfam
Module neighborhood information for Cj1731c

Cj1731c has total of 18 gene neighbors in modules 135, 154
Gene neighbors (18)
Gene Common Name Description Module membership
Cj0014c Cj0014c putative integral membrane protein (NCBI ptt file) 39, 135
Cj0178 Cj0178 putative outer membrane siderophore receptor (NCBI ptt file) 66, 154
Cj0179 exbB1 biopolymer transport protein (NCBI ptt file) 32, 154
Cj0203 Cj0203 putative transmembrane transport protein (NCBI ptt file) 32, 154
Cj0468 Cj0468 amino-acid ABC transporter integral membrane protein (NCBI ptt file) 117, 135
Cj0469 Cj0469 amino-acid ABC transporter ATP-binding protein (NCBI ptt file) 80, 135
Cj0874c Cj0874c cytochrome C (NCBI ptt file) 52, 154
Cj0920c Cj0920c putative ABC-type amino-acid transporter permease protein (NCBI ptt file) 98, 135
Cj0921c peb1A probable ABC-type amino-acid transporter periplasmic solute-binding protein (NCBI ptt file) 97, 135
Cj0934c Cj0934c putative transmembrane transport protein (NCBI ptt file) 81, 154
Cj0935c Cj0935c putative transmembrane transport protein (NCBI ptt file) 46, 154
Cj0960c rnpA putative ribonuclease P protein component (NCBI ptt file) 47, 135
Cj0977 Cj0977 hypothetical protein Cj0977 (NCBI ptt file) 140, 154
Cj1521c Cj1521c hypothetical protein Cj1521c (NCBI ptt file) 57, 154
Cj1608 Cj1608 possible two-component regulator (NCBI ptt file) 149, 154
Cj1718c leuB 3-isopropylmalate dehydrogenase (NCBI ptt file) 18, 135
Cj1724c Cj1724c hypothetical protein Cj1724c (NCBI ptt file) 89, 154
Cj1731c ruvC crossover junction endodeoxyribonuclease (NCBI ptt file) 135, 154
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 Cj1731c
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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