Organism : Campylobacter jejuni | Module List :
Cj1205c radA

putative DNA repair protein RadA (ATP-dependant protease) (NCBI ptt file)

CircVis
Functional Annotations (16)
Function System
Predicted ATP-dependent serine protease cog/ cog
DNA helicase activity go/ molecular_function
damaged DNA binding go/ molecular_function
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
ATP-dependent peptidase activity go/ molecular_function
serine-type endopeptidase activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
proteolysis go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
cobyrinic acid a,c-diamide synthase activity go/ molecular_function
sms tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1205c
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj1205c!

Warning: Cj1205c 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
7454 1.80e+03 TTAagGcATagcA
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7455 8.30e+03 GGGAAG
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7502 3.30e+04 GCaATGcCC
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7503 3.80e+04 GAAAGGAC
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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 Cj1205c

Cj1205c is enriched for 16 functions in 3 categories.
Enrichment Table (16)
Function System
Predicted ATP-dependent serine protease cog/ cog
DNA helicase activity go/ molecular_function
damaged DNA binding go/ molecular_function
methylated-DNA-[protein]-cysteine S-methyltransferase activity go/ molecular_function
ATP-dependent peptidase activity go/ molecular_function
serine-type endopeptidase activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA repair go/ biological_process
DNA recombination go/ biological_process
proteolysis go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
cobalamin biosynthetic process go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
cobyrinic acid a,c-diamide synthase activity go/ molecular_function
sms tigr/ tigrfam
Module neighborhood information for Cj1205c

Cj1205c has total of 35 gene neighbors in modules 36, 60
Gene neighbors (35)
Gene Common Name Description Module membership
Cj0040 Cj0040 hypothetical protein Cj0040 (NCBI ptt file) 36, 42
Cj0041 Cj0041 hypothetical protein Cj0041 (NCBI ptt file) 19, 36
Cj0080 Cj0080 putative membrane protein (NCBI ptt file) 44, 60
Cj0106 atpG ATP synthase F1 sector gamma subunit (NCBI ptt file) 60, 110
Cj0223 Cj0223 None 60, 71
Cj0385c Cj0385c putative integral membrane protein (NCBI ptt file) 60, 82
Cj0386 Cj0386 putative GTP-binding protein (NCBI ptt file) 36, 106
Cj0405 aroE shikimate 5-dehydrogenase (NCBI ptt file) 60, 165
Cj0413 Cj0413 putative periplasmic protein (NCBI ptt file) 36, 162
Cj0592c Cj0592c putative periplasmic protein (NCBI ptt file) 45, 60
Cj0619 Cj0619 putative integral membrane protein (NCBI ptt file) 60, 144
Cj0742 Cj0742 None 36, 71
Cj0767c kdtB 3-deoxy-D-manno-octulosonic-acid transferase (NCBI ptt file) 36, 60
Cj0774c Cj0774c ABC transport system ATP-binding protein (NCBI ptt file) 36, 167
Cj0866 Cj0866 None 36, 167
Cj0923c cheR putative MCP protein methyltransferase (NCBI ptt file) 60, 110
Cj0962 Cj0962 putative acetyltransferase (NCBI ptt file) 47, 60
Cj0963 Cj0963 hypothetical protein Cj0963 (NCBI ptt file) 37, 60
Cj0997 Cj0997 gidB homolog (NCBI ptt file) 36, 46
Cj1055c Cj1055c putative integral membrane protein (NCBI ptt file) 6, 36
Cj1077 Cj1077 putative periplasmic protein (NCBI ptt file) 36, 162
Cj1097 Cj1097 putative transmembrane transport protein (NCBI ptt file) 37, 60
Cj1114c pssA CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 60, 150
Cj1117c prmA possible ribosomal protein methyltransferase (NCBI ptt file) 60, 160
Cj1139c Cj1139c putative galactosyltransferase (NCBI ptt file) 36, 71
Cj1205c radA putative DNA repair protein RadA (ATP-dependant protease) (NCBI ptt file) 36, 60
Cj1370 Cj1370 putative nucleotide phosphoribosyltransferase (NCBI ptt file) 36, 46
Cj1426c Cj1426c hypothetical protein Cj1426c (NCBI ptt file) 17, 36
Cj1431c Cj1431c hypothetical protein Cj1431c (NCBI ptt file) 36, 42
Cj1432c Cj1432c putative sugar transferase (NCBI ptt file) 60, 109
Cj1433c Cj1433c hypothetical protein Cj1433c (NCBI ptt file) 19, 36
Cj1435c Cj1435c hypothetical protein Cj1435c (NCBI ptt file) 60, 150
Cj1442c Cj1442c hypothetical protein Cj1442c (NCBI ptt file) 6, 60
Cj1492c Cj1492c putative two-component sensor (NCBI ptt file) 38, 60
Cj1549c Cj1549c putative type I restriction enzyme R protein (NCBI ptt file) 46, 60
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 Cj1205c
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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