Organism : Campylobacter jejuni | Module List :
Cj1603 hisF

cyclase (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
Imidazoleglycerol-phosphate synthase cog/ cog
histidine biosynthetic process go/ biological_process
imidazoleglycerol-phosphate synthase activity go/ molecular_function
cytoplasm go/ cellular_component
imidazoleglycerol-phosphate synthase complex go/ cellular_component
Histidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hisF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1603
(Mouseover regulator name to see its description)

Cj1603 is regulated by 4 influences and regulates 0 modules.
Regulators for Cj1603 hisF (4)
Regulator Module Operator
Cj0287c 13 tf
Cj0400 13 tf
Cj0571 13 tf
Cj0757 13 tf

Warning: Cj1603 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
7408 3.30e+01 gCttagAcgcaACggg
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7409 4.30e+02 gcCTgT.Ac.CAag.gccCG
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7636 1.90e+03 A.cttt.tcCaAaAtcTtAcc
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7637 3.90e+04 aGTGGG
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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 Cj1603

Cj1603 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Imidazoleglycerol-phosphate synthase cog/ cog
histidine biosynthetic process go/ biological_process
imidazoleglycerol-phosphate synthase activity go/ molecular_function
cytoplasm go/ cellular_component
imidazoleglycerol-phosphate synthase complex go/ cellular_component
Histidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hisF tigr/ tigrfam
Module neighborhood information for Cj1603

Cj1603 has total of 34 gene neighbors in modules 13, 127
Gene neighbors (34)
Gene Common Name Description Module membership
Cj0019c Cj0019c MCP-domain signal transduction protein (NCBI ptt file) 13, 46
Cj0069 Cj0069 hypothetical protein Cj0069 (NCBI ptt file) 69, 127
Cj0103 atpF ATP synthase F0 sector B subunit (NCBI ptt file) 125, 127
Cj0114 Cj0114 putative periplasmic protein (NCBI ptt file) 91, 127
Cj0144 Cj0144 methyl-accepting chemotaxis signal transduction protein (NCBI ptt file) 8, 127
Cj0333c fdxA ferredoxin (NCBI ptt file) 13, 91
Cj0371 Cj0371 putative flagellar motility protein (NCBI ptt file) 13, 110
Cj0372 Cj0372 hypothetical protein Cj0372 (NCBI ptt file) 13, 18
Cj0373 Cj0373 putative D-2-hydroxyacid dehydrogenase (NCBI ptt file) 13, 81
Cj0374 Cj0374 hypothetical protein Cj0374 (NCBI ptt file) 13, 56
Cj0375 Cj0375 putative lipoprotein (NCBI ptt file) 13, 56
Cj0376 Cj0376 putative periplasmic protein (NCBI ptt file) 13, 17
Cj0377 Cj0377 probable AAA family ATPase (NCBI ptt file) 13, 77
Cj0401 lysS lysyl-tRNA synthetase (NCBI ptt file) 42, 127
Cj0403 Cj0403 hypothetical protein Cj0403 (NCBI ptt file) 127, 170
Cj0420 Cj0420 putative periplasmic protein (NCBI ptt file) 102, 127
Cj0453 thiC thiamin biosynthesis protein ThiC (NCBI ptt file) 13, 137
Cj0519 Cj0519 hypothetical protein Cj0519 (NCBI ptt file) 13, 108
Cj0575 ilvH acetolactate synthase small subunit (NCBI ptt file) 13, 110
Cj0604 Cj0604 hypothetical protein Cj0604 (NCBI ptt file) 119, 127
Cj0726c corA magnesium and cobalt transport protein (NCBI ptt file) 86, 127
Cj0806 dapA dihydrodipicolinate synthase (NCBI ptt file) 127, 137
Cj0901 Cj0901 putative amino acid ABC tansporter permease protein (NCBI ptt file) 92, 127
Cj1074c Cj1074c putative lipoprotein (NCBI ptt file) 13, 114
Cj1119c wlaM putative integral membrane protein (NCBI ptt file) 41, 127
Cj1120c wlaL putative sugar epimerase/dehydratase (NCBI ptt file) 127, 157
Cj1121c wlaK putative aminotransferase (degT family) (NCBI ptt file) 118, 127
Cj1154c Cj1154c small hydrophobic protein (NCBI ptt file) 47, 127
Cj1317 neuB3 N-acetylneuraminic acid synthetase (NCBI ptt file) 65, 127
Cj1420c Cj1420c hypothetical protein Cj1420c (NCBI ptt file) 120, 127
Cj1485c Cj1485c putative periplasmic protein (NCBI ptt file) 13, 52
Cj1502c putP sodium/proline symporter (NCBI ptt file) 91, 127
Cj1516 Cj1516 putative periplasmic oxidoreductase (NCBI ptt file) 127, 161
Cj1603 hisF cyclase (NCBI ptt file) 13, 127
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 Cj1603
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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