Organism : Campylobacter jejuni | Module List :
Cj0322 perR

peroxide stress regulator (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0322
(Mouseover regulator name to see its description)

Cj0322 is regulated by 2 influences and regulates 8 modules.
Regulators for Cj0322 perR (2)
Regulator Module Operator
Cj0322 140 tf
Cj1230 140 tf

Warning: Cj0322 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
7644 5.40e+03 GGCTGc
Loader icon
7645 1.10e+04 cGCTAAAAAGcG
Loader icon
7662 4.70e+02 CaAgCCC.gc
Loader icon
7663 2.00e+03 GcGTGG
Loader icon
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 Cj0322

Cj0322 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for Cj0322

Cj0322 has total of 21 gene neighbors in modules 131, 140
Gene neighbors (21)
Gene Common Name Description Module membership
Cj0056c Cj0056c hypothetical protein Cj0056c (NCBI ptt file) 140, 159
Cj0145 Cj0145 hypothetical protein Cj0145 (NCBI ptt file) 40, 131
Cj0288c lpxB lipid-A-disaccharide synthase (NCBI ptt file) 131, 153
Cj0322 perR peroxide stress regulator (NCBI ptt file) 131, 140
Cj0559 Cj0559 oxidoreductase (NCBI ptt file) 140, 157
Cj0690c Cj0690c possible restriction /modification enzyme (NCBI ptt file) 140, 161
Cj0819 Cj0819 small hydrophobic protein (NCBI ptt file) 25, 131
Cj0908 Cj0908 putative periplasmic protein (NCBI ptt file) 131, 134
Cj0977 Cj0977 hypothetical protein Cj0977 (NCBI ptt file) 140, 154
Cj0993c Cj0993c hypothetical protein Cj0993c (NCBI ptt file) 49, 131
Cj1041c Cj1041c putative periplasmic ATP/GTP-binding protein (NCBI ptt file) 61, 131
Cj1056c Cj1056c hypothetical protein Cj1056c (NCBI ptt file) 25, 131
Cj1067 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (NCBI ptt file) 111, 140
Cj1116c ftsH membrane bound zinc metallopeptidase (NCBI ptt file) 17, 131
Cj1159c Cj1159c small hydrophobic protein (NCBI ptt file) 124, 131
Cj1315c Cj1315c amidotransferase (NCBI ptt file) 131, 136
Cj1548c Cj1548c putative NADP-dependent alcohol dehydrogenase (NCBI ptt file) 31, 131
Cj1612 prfA peptide chain release factor 1 (NCBI ptt file) 77, 131
Cj1629 exbD2 putative exbD/tolR family transport protein (NCBI ptt file) 107, 131
Cj1635c rnc ribonuclease III (NCBI ptt file) 118, 140
Cj1721c Cj1721c possible outer membrane protein (NCBI ptt file) 112, 131
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 Cj0322
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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