Organism : Campylobacter jejuni | Module List :
Cj1636c rnhA

ribonuclease HI (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Ribonuclease HI cog/ cog
nucleic acid binding go/ molecular_function
ribonuclease H activity go/ molecular_function
DNA replication kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1636c
(Mouseover regulator name to see its description)

Cj1636c is regulated by 1 influences and regulates 0 modules.
Regulators for Cj1636c rnhA (1)
Regulator Module Operator
Cj0480c 118 tf

Warning: Cj1636c 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
7540 5.70e+02 CAAGGGTGC
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7541 9.60e+02 TGCGGG
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7618 8.20e+02 Tta.AaAaAgg
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7619 1.80e+03 TTtcACtCtCacaac
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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 Cj1636c

Cj1636c is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Ribonuclease HI cog/ cog
nucleic acid binding go/ molecular_function
ribonuclease H activity go/ molecular_function
DNA replication kegg/ kegg pathway
Module neighborhood information for Cj1636c

Cj1636c has total of 32 gene neighbors in modules 79, 118
Gene neighbors (32)
Gene Common Name Description Module membership
Cj0157c Cj0157c putative integral membrane protein (NCBI ptt file) 52, 118
Cj0191c def polypeptide deformylase (NCBI ptt file) 52, 118
Cj0241c Cj0241c putative iron-binding protein (NCBI ptt file) 18, 79
Cj0304c bioC putative biotin synthesis protein (NCBI ptt file) 41, 79
Cj0305c Cj0305c hypothetical protein Cj0305c (NCBI ptt file) 79, 144
Cj0327 Cj0327 hypothetical protein Cj0327 (NCBI ptt file) 118, 138
Cj0630c Cj0630c hypothetical protein Cj0630c (NCBI ptt file) 72, 79
Cj0637c mrsA putative peptide methionine sulfoxide reductase (NCBI ptt file) 79, 153
Cj0651 Cj0651 putative integral membrane protein (NCBI ptt file) 6, 118
Cj0694 Cj0694 putative periplasmic protein (NCBI ptt file) 14, 118
Cj0880c Cj0880c hypothetical protein Cj0880c (NCBI ptt file) 79, 88
Cj0982c Cj0982c putative amino-acid transporter periplasmic solute-binding protein (NCBI ptt file) 91, 118
Cj1080c Cj1080c hypothetical protein Cj1080c (NCBI ptt file) 118, 148
Cj1082c thiD phosphomethylpyrimidine kinase (NCBI ptt file) 65, 118
Cj1087c Cj1087c putative periplasmic protein (NCBI ptt file) 68, 118
Cj1089c Cj1089c hypothetical protein Cj1089c (NCBI ptt file) 18, 118
Cj1090c Cj1090c putative lipoprotein (NCBI ptt file) 65, 118
Cj1091c leuS leucyl-tRNA synthetase (NCBI ptt file) 18, 118
Cj1094c Cj1094c putative membrane protein (NCBI ptt file) 111, 118
Cj1104 Cj1104 hypothetical proteinCj1104 (NCBI ptt file) 79, 81
Cj1121c wlaK putative aminotransferase (degT family) (NCBI ptt file) 118, 127
Cj1124c wlaH putative galactosyltransferase (NCBI ptt file) 109, 118
Cj1128c wlaD putative glycosyltransferase (NCBI ptt file) 118, 138
Cj1243 hemE uroporphyrinogen decarboxylase (NCBI ptt file) 118, 138
Cj1388 Cj1388 hypothetical protein Cj1388 (NCBI ptt file) 111, 118
Cj1484c Cj1484c putative membrane protein (NCBI ptt file) 79, 92
Cj1635c rnc ribonuclease III (NCBI ptt file) 118, 140
Cj1636c rnhA ribonuclease HI (NCBI ptt file) 79, 118
Cj1645 tkt transketolase (NCBI ptt file) 70, 118
Cj1685c bioB putative biotin synthase (NCBI ptt file) 61, 79
Cj1712 Cj1712 hypothetical protein Cj1712 (NCBI ptt file) 79, 153
Cj1722c Cj1722c hypothetical protein Cj1722c (NCBI ptt file) 88, 118
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 Cj1636c
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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