Organism : Campylobacter jejuni | Module List :
Cj0498 trpC

indole-3-glycerol phosphate synthase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Indole-3-glycerol phosphate synthase cog/ cog
indole-3-glycerol-phosphate synthase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0498
(Mouseover regulator name to see its description)

Cj0498 is regulated by 4 influences and regulates 0 modules.
Regulators for Cj0498 trpC (4)
Regulator Module Operator
Cj0382c 133 tf
Cj0400 133 tf
Cj0440c 133 tf
Cj1273c 133 tf

Warning: Cj0498 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
7582 2.40e+02 GCTcAGctGg
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7583 3.50e+02 caaaGagTGAa
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7648 2.50e+03 GCTCAGCaGG
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7649 6.70e+03 GAGaaCcTGaGtTcGaATCaCccC
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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 Cj0498

Cj0498 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Indole-3-glycerol phosphate synthase cog/ cog
indole-3-glycerol-phosphate synthase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for Cj0498

Cj0498 has total of 43 gene neighbors in modules 100, 133
Gene neighbors (43)
Gene Common Name Description Module membership
CRISPR 100, 130
Cj0060c fliM flagellar motor switch protein (NCBI ptt file) 24, 100
Cj0129c Cj0129c outer membrane protein (NCBI ptt file) 14, 133
Cj0231c nrdB ribonucleoside-diphosphate reductase beta chain (NCBI ptt file) 133, 138
Cj0236c Cj0236c putative integral membrane protein (NCBI ptt file) 114, 133
Cj0268c Cj0268c putative transmembrane protein (NCBI ptt file) 111, 133
Cj0352 Cj0352 putative transmembrane protein (NCBI ptt file) 71, 100
Cj0392c pyk pyruvate kinase (NCBI ptt file) 91, 133
Cj0436 Cj0436 hypothetical protein Cj0436 (NCBI ptt file) 66, 133
Cj0495 Cj0495 hypothetical protein Cj0495 (NCBI ptt file) 100, 116
Cj0496 Cj0496 hypothetical protein Cj0496 (NCBI ptt file) 35, 133
Cj0497 Cj0497 putative lipoprotein (NCBI ptt file) 50, 100
Cj0498 trpC indole-3-glycerol phosphate synthase (NCBI ptt file) 100, 133
Cj0499 Cj0499 HIT-like protein (NCBI ptt file) 106, 133
Cj0632 ilvC ketol-acid reductoisomerase (NCBI ptt file) 102, 133
Cj0678 Cj0678 None 96, 100
Cj0686 gcpE gcpE protein homolog (NCBI ptt file) 42, 100
Cj0740 Cj0740 hypothetical protein Cj0740 (NCBI ptt file) 33, 100
Cj0896c pheT phenylalanyl-tRNA synthetase beta chain (NCBI ptt file) 58, 133
Cj0931c argH argininosuccinate lyase (NCBI ptt file) 86, 133
Cj0932c pckA phosphoenolpyruvate carboxykinase (ATP) (NCBI ptt file) 102, 133
Cj0933c pycB putative pyruvate carboxylase B subunit (NCBI ptt file) 69, 133
Cj0936 atpE ATP synthase F0 sector C subunit (NCBI ptt file) 111, 133
Cj0986c Cj0986c putative integral membrane protein (NCBI ptt file) 26, 133
Cj0998c Cj0998c putative periplasmic protein (NCBI ptt file) 21, 133
Cj1020c Cj1020c putative cytochrome C (NCBI ptt file) 98, 133
Cj1068 Cj1068 putative integral membrane protein (NCBI ptt file) 66, 100
Cj1093c secD protein-export membrane protein (NCBI ptt file) 14, 133
Cj1126c wlaF putative integral membrane protein (possible oligosaccharyl transferase) (NCBI ptt file) 117, 133
Cj1131c galE UDP-glucose 4-epimerase (NCBI ptt file) 111, 133
Cj1133 waaC putative lipopolysaccharide heptosyltransferase (NCBI ptt file) 100, 101
Cj1164c Cj1164c hypothetical protein Cj1164c (NCBI ptt file) 98, 133
Cj1300 Cj1300 hypothetical protein Cj1300 (NCBI ptt file) 133, 165
Cj1364c fumC fumarate hydratase (NCBI ptt file) 102, 133
Cj1395 Cj1395 None 100, 107
Cj1444c kpsD putative capsule polysaccharide export system periplasmic protein (NCBI ptt file) 88, 133
Cj1518 moaE possible molybdopterin converting factor, subunit 2 (NCBI ptt file) 133, 137
Cj1600 hisH amidotransferase HisH (NCBI ptt file) 133, 141
Cj1626c Cj1626c putative periplasmic protein (NCBI ptt file) 86, 133
Cj1675 fliQ flagellar biosynthetic protein (NCBI ptt file) 26, 133
Cjp14 tRNA-Ala tRNA-Ala (NCBI) 16, 100
Cjp15 tRNA-Ile tRNA-Ile (NCBI) 100, 105
Cjr01 rrs 16S ribosomal RNA (NCBI) 100, 144
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 Cj0498
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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