Organism : Campylobacter jejuni | Module List :
Cj1582c

putative peptide ABC-transport system permease protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1582c
(Mouseover regulator name to see its description)

Cj1582c is regulated by 5 influences and regulates 0 modules.
Regulators for Cj1582c (5)
Regulator Module Operator
Cj0123c 71 tf
Cj0368c 71 tf
Cj1349c 71 tf
Cj1556 71 tf
Cj0480c 164 tf

Warning: Cj1582c 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
7524 5.30e+01 g.ggTgcgGtAgt.gg
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7525 7.30e+02 gTgCtT.tggtgaTaatTgc
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7710 1.10e+02 TtA.agCtAaAgaAa..gCT
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7711 6.50e+03 GcAGTGAAGc
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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 Cj1582c

Cj1582c is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for Cj1582c

Cj1582c has total of 37 gene neighbors in modules 71, 164
Gene neighbors (37)
Gene Common Name Description Module membership
Cj0058 Cj0058 putative periplasmic protein (NCBI ptt file) 162, 164
Cj0072c Cj0072c None 38, 164
Cj0223 Cj0223 None 60, 71
Cj0261c Cj0261c hypothetical protein Cj0261c (NCBI ptt file) 57, 164
Cj0308c bioD putative dethiobiotin synthetase (NCBI ptt file) 6, 164
Cj0323 Cj0323 hypothetical protein Cj0323 (NCBI ptt file) 15, 71
Cj0352 Cj0352 putative transmembrane protein (NCBI ptt file) 71, 100
Cj0390 Cj0390 putative transmembrane protein (NCBI ptt file) 46, 71
Cj0412 Cj0412 putative ATP /GTP binding protein (NCBI ptt file) 71, 108
Cj0566 Cj0566 hypothetical protein Cj0566 (NCBI ptt file) 71, 162
Cj0588 tlyA putative haemolysin (NCBI ptt file) 71, 72
Cj0730 Cj0730 putative ABC transport system permease (NCBI ptt file) 63, 164
Cj0742 Cj0742 None 36, 71
Cj0748 Cj0748 hypothetical protein Cj0748 (NCBI ptt file) 71, 152
Cj0752 Cj0752 None 11, 164
Cj0768c Cj0768c putative decarboxylase (NCBI ptt file) 71, 72
Cj0788 Cj0788 hypothetical protein Cj0788 (NCBI ptt file) 24, 164
Cj0792 Cj0792 hypothetical protein Cj0792 (NCBI ptt file) 89, 164
Cj0793 Cj0793 signal transduction histidine kinase (NCBI ptt file) 24, 164
Cj0795c murF putative UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-- ligase (NCBI ptt file) 122, 164
Cj0823 Cj0823 hypothetical protein Cj0823 (NCBI ptt file) 104, 164
Cj0879c Cj0879c putative periplasmic protein (NCBI ptt file) 116, 164
Cj0946 Cj0946 putative lipoprotein (NCBI ptt file) 71, 72
Cj0990c Cj0990c hypothetical protein Cj0990c (NCBI ptt file) 122, 164
Cj1069 Cj1069 hypothetical protein Cj1069 (NCBI ptt file) 71, 72
Cj1076 proC putative pyrroline-5-carboxylate reductase (NCBI ptt file) 71, 72
Cj1098 pyrB aspartate carbamoyltransferase (NCBI ptt file) 71, 167
Cj1139c Cj1139c putative galactosyltransferase (NCBI ptt file) 36, 71
Cj1244 Cj1244 hypothetical protein Cj1244 (NCBI ptt file) 143, 164
Cj1268c Cj1268c hypothetical protein Cj1268c (NCBI ptt file) 71, 162
Cj1351 pldA phospholipase A (NCBI ptt file) 124, 164
Cj1538c Cj1538c putative anion-uptake ABC-transport system ATP-binding protein (NCBI ptt file) 162, 164
Cj1582c Cj1582c putative peptide ABC-transport system permease protein (NCBI ptt file) 71, 164
Cj1652c murI glutamate racemase (NCBI ptt file) 1, 164
Cj1720 Cj1720 hypothetical protein Cj1720 (NCBI ptt file) 38, 71
Cjp23 tRNA-Met tRNA-Met (NCBI) 124, 164
Cjp27 tRNA-Gly tRNA-Gly (NCBI) 73, 164
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 Cj1582c
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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