Organism : Campylobacter jejuni | Module List :
Cj0719c

hypothetical protein Cj0719c (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted enzyme with a TIM-barrel fold cog/ cog
TIGR00044 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0719c
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0719c!

Warning: Cj0719c 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
7516 5.40e+01 TT.AAgGaAAAA
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7517 3.40e+03 CaCcTGcAac
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7560 1.70e+00 CcTGCtg.ca.agTaGcagCG
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7561 8.00e+02 cCAcCaTGC
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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 Cj0719c

Cj0719c is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted enzyme with a TIM-barrel fold cog/ cog
TIGR00044 tigr/ tigrfam
Module neighborhood information for Cj0719c

Cj0719c has total of 41 gene neighbors in modules 67, 89
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0001 dnaA chromosomal replication initiator protein (NCBI ptt file) 51, 89
Cj0161c moaA molybdenum cofactor biosynthesis protein A (NCBI ptt file) 89, 155
Cj0316 pheA chorismate mutaseprephenate dehydratase (VIMSS-AUTO) 24, 89
Cj0356c Cj0356c hypothetical protein Cj0356c (NCBI ptt file) 67, 161
Cj0525c pbpB putative penicillin-binding protein (NCBI ptt file) 53, 89
Cj0540 Cj0540 hypothetical protein Cj0540 (NCBI ptt file) 26, 89
Cj0562 dnaB replicative DNA helicase (NCBI ptt file) 89, 116
Cj0593c Cj0593c putative integral membrane protein (NCBI ptt file) 25, 89
Cj0594c Cj0594c putative periplasmic protein (NCBI ptt file) 89, 92
Cj0595c nth endonuclease III (NCBI ptt file) 89, 116
Cj0719c Cj0719c hypothetical protein Cj0719c (NCBI ptt file) 67, 89
Cj0724 Cj0724 hypothetical protein Cj0724 (NCBI ptt file) 67, 144
Cj0764c speA biosynthetic arginine decarboxylase (NCBI ptt file) 68, 89
Cj0792 Cj0792 hypothetical protein Cj0792 (NCBI ptt file) 89, 164
Cj0794 Cj0794 hypothetical protein Cj0794 (NCBI ptt file) 67, 167
Cj0827 truA putative tRNA pseudouridine synthase (NCBI ptt file) 89, 104
Cj0862c pabB para-aminobenzoate synthase component I (NCBI ptt file) 17, 89
Cj0865 dsbB putative disulfide oxidoreductase (NCBI ptt file) 67, 89
Cj0911 Cj0911 putative periplasmic protein (NCBI ptt file) 39, 89
Cj0937 Cj0937 putative integral membrane protein (NCBI ptt file) 67, 144
Cj0979c Cj0979c putative secreted nuclease (NCBI ptt file) 67, 129
Cj1005c Cj1005c putative membrane bound ATPase (NCBI ptt file) 49, 89
Cj1006c Cj1006c hypothetical proteinCj1006c (NCBI ptt file) 59, 89
Cj1007c Cj1007c putative membrane protein (NCBI ptt file) 49, 89
Cj1008c aroB 3-dehydroquinate synthase (NCBI ptt file) 49, 89
Cj1009c Cj1009c hypothetical protein Cj1009c (NCBI ptt file) 49, 89
Cj1034c Cj1034c possible dnaJ-like protein (NCBI ptt file) 62, 67
Cj1099 Cj1099 peptidase (M3 family) (NCBI ptt file) 46, 89
Cj1142 neuC1 putative N-acetylglucosamine-6-phosphate 2-epimerase/N-acetylglucosamine-6-phosphatase (NCBI ptt file) 45, 67
Cj1211 Cj1211 putative integral membrane protein (NCBI ptt file) 67, 77
Cj1219c Cj1219c putative periplasmic protein (NCBI ptt file) 50, 67
Cj1249 Cj1249 hypothetical protein Cj1249 (NCBI ptt file) 27, 67
Cj1304 acpP3 putative acyl carrier protein (NCBI ptt file) 77, 89
Cj1307 Cj1307 putative amino acid activating enzyme (NCBI ptt file) 67, 121
Cj1452 Cj1452 putative integral membrane protein (NCBI ptt file) 23, 89
Cj1466 flgK putative flagellar hook-associated protein (NCBI ptt file) 67, 86
Cj1531 dapF putative diaminopimelate epimerase (NCBI ptt file) 10, 67
Cj1545c Cj1545c MdaB protein homolog (NCBI ptt file) 67, 83
Cj1565c pflA paralysed flagellum protein (NCBI ptt file) 7, 67
Cj1724c Cj1724c hypothetical protein Cj1724c (NCBI ptt file) 89, 154
Cj1726c metA putative homoserine O-succinyltransferase (NCBI ptt file) 50, 89
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 Cj0719c
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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