Organism : Campylobacter jejuni | Module List :
Cj0716

putative phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase cog/ cog
3-deoxy-7-phosphoheptulonate synthase activity go/ molecular_function
aromatic amino acid family biosynthetic process go/ biological_process
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
DAHP_synth_II tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0716
(Mouseover regulator name to see its description)

Cj0716 is regulated by 4 influences and regulates 0 modules.
Regulators for Cj0716 (4)
Regulator Module Operator
Cj0287c 137 tf
Cj0518 137 tf
Cj1273c 98 tf
Cj1552c 98 tf

Warning: Cj0716 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
7578 1.60e+05 CCAAaaCC
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7579 2.90e+04 CGaAAGCAC
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7656 1.30e+04 TGgtaaTtTcCcgatt.GcTtgG
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7657 1.20e+04 GCAGGAG
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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 Cj0716

Cj0716 is enriched for 7 functions in 3 categories.
Module neighborhood information for Cj0716

Cj0716 has total of 56 gene neighbors in modules 98, 137
Gene neighbors (56)
Gene Common Name Description Module membership
Cj0020c Cj0020c cytochrome C551 peroxidase (NCBI ptt file) 137, 170
Cj0067 Cj0067 hypothetical protein Cj0067 (NCBI ptt file) 98, 104
Cj0105 atpA ATP synthase F1 sector alpha subunit (NCBI ptt file) 91, 137
Cj0172c Cj0172c hypothetical protein Cj0172c (NCBI ptt file) 61, 137
Cj0205 bacA putative undecaprenol kinase (bacitracin resistance protein) (NCBI ptt file) 98, 110
Cj0256 Cj0256 putative integral membrane protein (NCBI ptt file) 31, 98
Cj0266c Cj0266c putative integral membrane protein (NCBI ptt file) 53, 98
Cj0298c panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI ptt file) 98, 142
Cj0381c pyrF orotidine 5'-phosphate decarboxylase (NCBI ptt file) 81, 98
Cj0404 Cj0404 putative transmembrane protein (NCBI ptt file) 98, 170
Cj0442 fabF 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) 83, 98
Cj0452 dnaQ exonuclease, possibly dna polymerase III epsilon subunit (NCBI ptt file) 51, 98
Cj0453 thiC thiamin biosynthesis protein ThiC (NCBI ptt file) 13, 137
Cj0512 purC phosphoribosylaminoimidazole-succinocarboxamide synthase (NCBI ptt file) 111, 137
Cj0518 htpG hsp90 family heat shock protein (NCBI ptt file) 111, 137
Cj0543 proS prolyl-tRNA synthetase (NCBI ptt file) 66, 98
Cj0545 hemC porphobilinogen deaminase (NCBI ptt file) 48, 137
Cj0662c hslU putative heat shock protein (NCBI ptt file) 137, 170
Cj0663c hslV putative heat shock protein (NCBI ptt file) 137, 160
Cj0664c rplI 50S ribosomal protein L9 (NCBI ptt file) 130, 137
Cj0665c argG argininosuccinate synthase (NCBI ptt file) 86, 98
Cj0672 Cj0672 putative periplasmic protein (NCBI ptt file) 26, 137
Cj0695 ftsA cell division protein ftsA (NCBI ptt file) 132, 137
Cj0714 rplS 50S ribosomal protein L19 (NCBI ptt file) 8, 137
Cj0716 Cj0716 putative phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI ptt file) 98, 137
Cj0806 dapA dihydrodipicolinate synthase (NCBI ptt file) 127, 137
Cj0807 Cj0807 putative oxidoreductase (NCBI ptt file) 111, 137
Cj0843c Cj0843c putative secreted transglycosylase (NCBI ptt file) 33, 98
Cj0858c murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 68, 98
Cj0898 Cj0898 HIT-family protein (NCBI ptt file) 98, 102
Cj0899c thiJ 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein (NCBI ptt file) 110, 137
Cj0920c Cj0920c putative ABC-type amino-acid transporter permease protein (NCBI ptt file) 98, 135
Cj0929 pepA aminopeptidase (NCBI ptt file) 53, 137
Cj0994c argF ornithine carbamoyltransferase (NCBI ptt file) 42, 137
Cj0995c hemB delta-aminolevulinic acid dehydratase (NCBI ptt file) 111, 137
Cj1020c Cj1020c putative cytochrome C (NCBI ptt file) 98, 133
Cj1075 Cj1075 hypothetical protein Cj1075 (NCBI ptt file) 137, 142
Cj1096c metK S-adenosylmethionine synthetase (NCBI ptt file) 137, 170
Cj1106 Cj1106 possible periplasmic thioredoxin (NCBI ptt file) 14, 98
Cj1164c Cj1164c hypothetical protein Cj1164c (NCBI ptt file) 98, 133
Cj1176c Cj1176c hypothetical protein Cj1176c (NCBI ptt file) 137, 142
Cj1224 Cj1224 putative iron-binding protein (NCBI ptt file) 66, 98
Cj1248 guaA GMP synthase (glutamine-hydrolyzing) (NCBI ptt file) 98, 170
Cj1400c fabI putative enoyl-[acyl-carrier-protein] reductase [NADH] (NCBI ptt file) 94, 137
Cj1401c tpiA putative triosephosphate isomerase (NCBI ptt file) 110, 137
Cj1403c gapA glyceraldehyde 3-phosphate dehydrogenase (NCBI ptt file) 137, 142
Cj1439c glf UDP-galactopyranose mutase (NCBI ptt file) 81, 98
Cj1441c kfiD putative UDP-glucose 6-dehydrogenase (NCBI ptt file) 14, 137
Cj1476c Cj1476c pyruvate-flavodoxin oxidoreductase (NCBI ptt file) 137, 170
Cj1495c Cj1495c hypothetical protein Cj1495c (NCBI ptt file) 14, 98
Cj1517 moaD possible molybdopterin converting factor, subunit 1 (NCBI ptt file) 98, 106
Cj1518 moaE possible molybdopterin converting factor, subunit 2 (NCBI ptt file) 133, 137
Cj1599 hisB imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file) 98, 138
Cj1639 Cj1639 nifU protein homolog (NCBI ptt file) 69, 137
Cj1671c Cj1671c hypothetical protein Cj1671c (NCBI ptt file) 66, 98
Cj1672c eno enolase (NCBI ptt file) 137, 160
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 Cj0716
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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