Organism : Campylobacter jejuni | Module List :
Cj1001 rpoD

RNA polymerase sigma factor (sigma-70) (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
RpoD_Cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1001
(Mouseover regulator name to see its description)

Cj1001 is regulated by 16 influences and regulates 2 modules.
Regulators for Cj1001 rpoD (16)
Regulator Module Operator
Cj0061c 53 tf
Cj0480c 53 tf
Cj1000 53 tf
Cj1230 53 tf
Cj1533c 53 tf
Cj0101 62 tf
Cj0460 62 tf
Cj0480c 62 tf
Cj0670 62 tf
Cj0757 62 tf
Cj1000 62 tf
Cj1001 62 tf
Cj1103 62 tf
Cj1253 62 tf
Cj1273c 62 tf
Cj1552c 62 tf

Warning: Cj1001 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
7488 3.70e+01 caagCTtcaaccaAaAcatctcC
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7489 9.70e+03 AaGGaAAaTatt.tttGATAtT
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7506 1.70e+03 aaaatTtgctAaAatttcagt
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7507 3.20e+03 CCGCTC
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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 Cj1001

Cj1001 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
RpoD_Cterm tigr/ tigrfam
Module neighborhood information for Cj1001

Cj1001 has total of 48 gene neighbors in modules 53, 62
Gene neighbors (48)
Gene Common Name Description Module membership
Cj0015c Cj0015c hypothetical protein Cj0015c (NCBI ptt file) 39, 62
Cj0023 purB adenylosuccinate lyase (NCBI ptt file) 62, 146
Cj0024 nrdA ribonucleoside-diphosphate reductase alpha chain (NCBI ptt file) 41, 62
Cj0131 Cj0131 putative periplasmic protein (NCBI ptt file) 49, 62
Cj0149c hom homoserine dehydrogenase (NCBI ptt file) 62, 165
Cj0266c Cj0266c putative integral membrane protein (NCBI ptt file) 53, 98
Cj0299 Cj0299 putative periplasmic beta-lactamase (NCBI ptt file) 19, 62
Cj0319 fliG flagellar motor switch protein (NCBI ptt file) 62, 156
Cj0402 glyA serine hydroxymethyltransferase (NCBI ptt file) 53, 82
Cj0431 Cj0431 putative periplasmic ATP /GTP-binding protein (NCBI ptt file) 57, 62
Cj0489 ald' putative aldehyde dehydrogenase N-terminus (RefSeq) 35, 53
Cj0506 alaS alanyl-tRNA synthetase (NCBI ptt file) 10, 53
Cj0507 maf MAF homolog (NCBI ptt file) 53, 157
Cj0525c pbpB putative penicillin-binding protein (NCBI ptt file) 53, 89
Cj0546 Cj0546 hypothetical protein Cj0546 (NCBI ptt file) 23, 62
Cj0676 Cj0676 None 53, 85
Cj0680c uvrB excinuclease ABC subunit B (NCBI ptt file) 50, 53
Cj0681 Cj0681 hypothetical protein Cj0681 (NCBI ptt file) 53, 155
Cj0682 Cj0682 hypothetical protein Cj0682 (NCBI ptt file) 33, 53
Cj0693c Cj0693c hypothetical protein Cj0693c (NCBI ptt file) 15, 62
Cj0706 Cj0706 hypothetical protein Cj0706 (NCBI ptt file) 62, 102
Cj0766c tmk putative thymidylate kinase (NCBI ptt file) 39, 62
Cj0828c ilvA threonine dehydratase biosynthetic (NCBI ptt file) 54, 62
Cj0832c Cj0832c putative integral membrane protein (NCBI ptt file) 53, 121
Cj0837c Cj0837c hypothetical protein Cj0837c (NCBI ptt file) 53, 105
Cj0839c Cj0839c hypothetical protein Cj0839c (NCBI ptt file) 10, 53
Cj0881c Cj0881c hypothetical protein Cj0881c (NCBI ptt file) 25, 53
Cj0924c cheB' putative MCP protein-glutamate methylesterase (NCBI ptt file) 53, 82
Cj0929 pepA aminopeptidase (NCBI ptt file) 53, 137
Cj0974 Cj0974 very hypothetical protein Cj0974 (NCBI ptt file) 29, 62
Cj1001 rpoD RNA polymerase sigma factor (sigma-70) (NCBI ptt file) 53, 62
Cj1034c Cj1034c possible dnaJ-like protein (NCBI ptt file) 62, 67
Cj1044c thiH thiH protein (NCBI ptt file) 49, 53
Cj1046c moeB putative molybdopterin biosynthesis protein (NCBI ptt file) 42, 53
Cj1129c wlaC putative glycosyltransferase (NCBI ptt file) 38, 62
Cj1130c wlaB ABC-type transport protein (NCBI ptt file) 62, 141
Cj1180c Cj1180c putative ABC transporter ATP binding protein (NCBI ptt file) 26, 62
Cj1215 Cj1215 putative periplasmic protein (NCBI ptt file) 62, 147
Cj1225 Cj1225 hypothetical protein Cj1225 (NCBI ptt file) 20, 53
Cj1264c hydD putative hydrogenase maturation protease (NCBI ptt file) 53, 162
Cj1279c Cj1279c putative fibronectin domain-containing lipoprotein (NCBI ptt file) 53, 74
Cj1371 Cj1371 putative periplasmic protein (vacJ homolog) (NCBI ptt file) 48, 62
Cj1404 Cj1404 hypothetical protein Cj1404 (NCBI ptt file) 53, 152
Cj1410c Cj1410c putative membrane protein (NCBI ptt file) 25, 53
Cj1471c Cj1471c putative type II protein secretion system E protein (NCBI ptt file) 62, 155
Cj1643 Cj1643 putative periplasmic protein (NCBI ptt file) 62, 141
Cj1653c Cj1653c probable lipoprotein (NCBI ptt file) 53, 144
Cj1674 Cj1674 hypothetical protein Cj1674 (NCBI ptt file) 53, 82
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 Cj1001
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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