Organism : Campylobacter jejuni | Module List :
Cj1263 recR

recombination protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Recombinational DNA repair protein (RecF pathway) cog/ cog
DNA repair go/ biological_process
DNA recombination go/ biological_process
Homologous recombination kegg/ kegg pathway
recR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1263
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj1263!

Warning: Cj1263 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
7522 8.70e+01 G.aGgtgcAAAA.g
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7523 4.10e+03 GAGCAGGc
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7594 9.00e+00 aaggaaaAaTataGc
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7595 2.70e+03 cCagttGAagCcAtT
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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 Cj1263

Cj1263 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Recombinational DNA repair protein (RecF pathway) cog/ cog
DNA repair go/ biological_process
DNA recombination go/ biological_process
Homologous recombination kegg/ kegg pathway
recR tigr/ tigrfam
Module neighborhood information for Cj1263

Cj1263 has total of 43 gene neighbors in modules 70, 106
Gene neighbors (43)
Gene Common Name Description Module membership
Cj0031 Cj0031 putative type IIS restriction/modification enzyme (NCBI) 106, 141
Cj0033 Cj0033 putative integral membrane protein (NCBI ptt file) 70, 162
Cj0280 Cj0280 hypothetical protein Cj0280 (NCBI ptt file) 51, 70
Cj0294 Cj0294 moeB/thiF family protein (NCBI ptt file) 6, 70
Cj0321 dxs 1-deoxyxylulose-5-phosphate synthase (NCBI ptt file) 70, 149
Cj0324 ubiE ubiquinonemenaquinone biosynthesis methlytransferase (VIMSS-AUTO) 7, 70
Cj0335 flhB flagellar biosynthetic protein (NCBI ptt file) 106, 129
Cj0386 Cj0386 putative GTP-binding protein (NCBI ptt file) 36, 106
Cj0455c Cj0455c putative membrane protein (NCBI ptt file) 46, 70
Cj0464 recG ATP-dependent DNA helicase (NCBI ptt file) 12, 106
Cj0499 Cj0499 HIT-like protein (NCBI ptt file) 106, 133
Cj0500 Cj0500 putative ATP /GTP binding protein (NCBI ptt file) 51, 106
Cj0556 Cj0556 hypothetical protein Cj0556 (NCBI ptt file) 6, 70
Cj0560 Cj0560 putative integral membrane protein (NCBI ptt file) 70, 162
Cj0569 Cj0569 hypothetical protein Cj0569 (NCBI ptt file) 51, 106
Cj0609c Cj0609c possible periplasmic protein (NCBI ptt file) 58, 70
Cj0634 Cj0634 SMF family protein (NCBI ptt file) 106, 109
Cj0648 Cj0648 hypothetical protein Cj0648 (NCBI ptt file) 70, 76
Cj0739 Cj0739 hypothetical protein Cj0739 (NCBI ptt file) 106, 116
Cj0846 Cj0846 putative integral membrane protein (NCBI ptt file) 6, 70
Cj0848c Cj0848c hypothetical protein Cj0848c (NCBI ptt file) 6, 70
Cj0930 Cj0930 putative GTP-binding protein (NCBI ptt file) 61, 70
Cj1043c Cj1043c possible transferase (NCBI ptt file) 43, 106
Cj1047c Cj1047c hypothetical protein Cj1047c (NCBI ptt file) 43, 106
Cj1048c dapE succinyl-diaminopimelate desuccinylase (NCBI ptt file) 51, 106
Cj1125c wlaG putative galactosyltransferase (NCBI ptt file) 106, 109
Cj1187c arsB putative arsenical pump membrane protein (NCBI ptt file) 70, 134
Cj1188c gidA glucose inhibited division protein A homolog (NCBI ptt file) 61, 70
Cj1236 Cj1236 hypothetical protein Cj1236 (NCBI ptt file) 72, 106
Cj1254 Cj1254 hypothetical protein Cj1254 (NCBI ptt file) 23, 106
Cj1263 recR recombination protein (NCBI ptt file) 70, 106
Cj1303 fabH2 putative 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) 106, 141
Cj1309c Cj1309c hypothetical protein Cj1309c (NCBI ptt file) 70, 125
Cj1343c Cj1343c putative periplasmic protein (NCBI ptt file) 92, 106
Cj1353 ceuC enterochelin uptake permease (NCBI ptt file) 3, 106
Cj1381 Cj1381 putative lipoprotein (NCBI ptt file) 70, 122
Cj1438c Cj1438c putative sugar transferase (NCBI ptt file) 70, 116
Cj1517 moaD possible molybdopterin converting factor, subunit 1 (NCBI ptt file) 98, 106
Cj1519 moeA2 putative molybdopterin biosynthesis protein (NCBI ptt file) 80, 106
Cj1645 tkt transketolase (NCBI ptt file) 70, 118
Cj1667c Cj1667c repA protein homolog (NCBI ptt file) 106, 129
Cj1713 Cj1713 hypothetical protein Cj1713 (NCBI ptt file) 70, 149
Cj1716c leuD putative 3-isopropylmalate dehydratase small subunit (NCBI ptt file) 17, 70
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 Cj1263
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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