Organism : Campylobacter jejuni | Module List :
Cj1238 pdxJ

putative pyridoxal phosphate biosynthetic protein (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Pyridoxal phosphate biosynthesis protein cog/ cog
catalytic activity go/ molecular_function
cytoplasm go/ cellular_component
pyridoxine biosynthetic process go/ biological_process
Vitamin B6 metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pdxJ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1238
(Mouseover regulator name to see its description)

Cj1238 is regulated by 3 influences and regulates 0 modules.
Regulators for Cj1238 pdxJ (3)
Regulator Module Operator
Cj0473 144 tf
Cj0670 144 tf
Cj1561 144 tf

Warning: Cj1238 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
7480 5.60e+03 GGCACG
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7481 2.10e+04 CccCaacTaCatTGCCAAC
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7670 3.30e+02 AAAA.tAattAAGGAAAaac
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7671 6.40e+00 ATAcCAAaaaAGTTcaAAAGaA
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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 Cj1238

Cj1238 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Pyridoxal phosphate biosynthesis protein cog/ cog
catalytic activity go/ molecular_function
cytoplasm go/ cellular_component
pyridoxine biosynthetic process go/ biological_process
Vitamin B6 metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
pdxJ tigr/ tigrfam
Module neighborhood information for Cj1238

Cj1238 has total of 47 gene neighbors in modules 49, 144
Gene neighbors (47)
Gene Common Name Description Module membership
Cj0131 Cj0131 putative periplasmic protein (NCBI ptt file) 49, 62
Cj0139 Cj0139 putative endonuclease (NCBI ptt file) 49, 152
Cj0305c Cj0305c hypothetical protein Cj0305c (NCBI ptt file) 79, 144
Cj0364 Cj0364 hypothetical protein Cj0364 (NCBI ptt file) 49, 68
Cj0370 rpsU 30S ribosomal protein S21 (NCBI ptt file) 49, 75
Cj0429c Cj0429c hypothetical protein Cj0429c (NCBI ptt file) 55, 144
Cj0568 Cj0568 hypothetical protein Cj0568 (NCBI ptt file) 49, 50
Cj0581 Cj0581 putative NTPase (NCBI ptt file) 49, 82
Cj0587 Cj0587 putative integral membrane protein (NCBI ptt file) 72, 144
Cj0599 Cj0599 putative periplasmic protein (NCBI ptt file) 45, 144
Cj0601c Cj0601c putative sodium-dependent transmembrane transport protein (NCBI ptt file) 22, 49
Cj0619 Cj0619 putative integral membrane protein (NCBI ptt file) 60, 144
Cj0699c glnA glutamine synthetase (NCBI ptt file) 49, 121
Cj0720c flaC flagellin (NCBI ptt file) 86, 144
Cj0721c Cj0721c putative integral membrane protein (NCBI ptt file) 97, 144
Cj0722c Cj0722c putative DNA methylase (NCBI ptt file) 101, 144
Cj0723c Cj0723c putative integral membrane zinc-metalloprotease (NCBI ptt file) 39, 144
Cj0724 Cj0724 hypothetical protein Cj0724 (NCBI ptt file) 67, 144
Cj0781 napG putative ferredoxin (NCBI ptt file) 49, 94
Cj0782 napH putative ferredoxin (NCBI ptt file) 49, 170
Cj0783 napB periplasmic nitrate reductase small subunit (cytochrome C-type protein) (NCBI ptt file) 49, 87
Cj0838c metS methionyl-tRNA synthetase (NCBI ptt file) 34, 49
Cj0872 dsbA putative protein disulphide isomerase (NCBI ptt file) 49, 58
Cj0889c Cj0889c putative sensory trasnduction histidine kinase (NCBI ptt file) 5, 144
Cj0937 Cj0937 putative integral membrane protein (NCBI ptt file) 67, 144
Cj0950c Cj0950c putative lipoprotein (NCBI ptt file) 33, 49
Cj0993c Cj0993c hypothetical protein Cj0993c (NCBI ptt file) 49, 131
Cj1005c Cj1005c putative membrane bound ATPase (NCBI ptt file) 49, 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
Cj1044c thiH thiH protein (NCBI ptt file) 49, 53
Cj1135 Cj1135 putative two-domain glycosyltransferase (NCBI ptt file) 45, 144
Cj1213c glcD putative glycolate oxidase subunit D (NCBI ptt file) 49, 68
Cj1237c Cj1237c possible phosphatase (NCBI ptt file) 144, 167
Cj1238 pdxJ putative pyridoxal phosphate biosynthetic protein (NCBI ptt file) 49, 144
Cj1239 pdxA putative pyridoxal phosphate biosynthetic protein (NCBI ptt file) 57, 144
Cj1316c Cj1316c hypothetical protein Cj1316c (NCBI ptt file) 63, 144
Cj1376 Cj1376 putative periplasmic protein (NCBI ptt file) 19, 144
Cj1457c Cj1457c ypothetical protein Cj1457c (NCBI ptt file) 144, 152
Cj1529c purM phosphoribosylformylglycinamidine cyclo-ligase (NCBI ptt file) 49, 94
Cj1543 Cj1543 hypothetical protein Cj1543 (NCBI ptt file) 116, 144
Cj1605c dapD possible 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI ptt file) 49, 68
Cj1651c map methionine aminopeptidase (NCBI ptt file) 19, 144
Cj1653c Cj1653c probable lipoprotein (NCBI ptt file) 53, 144
Cjr01 rrs 16S ribosomal RNA (NCBI) 100, 144
Cjr06 Cjr06 5S ribosomal RNA (NCBI) 49, 68
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 Cj1238
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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