Organism : Campylobacter jejuni | Module List :
Cj1643

putative periplasmic protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
protein binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1643
(Mouseover regulator name to see its description)

Cj1643 is regulated by 11 influences and regulates 0 modules.
Regulators for Cj1643 (11)
Regulator Module Operator
Cj0101 62 tf
Cj0460 62 tf
Cj0480c 62 tf
Cj0670 62 tf
Cj0757 62 tf
Cj1000 62 tf
Cj1001 62 tf
Cj1103 62 tf
Cj1253 62 tf
Cj1273c 62 tf
Cj1552c 62 tf

Warning: Cj1643 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
7506 1.70e+03 aaaatTtgctAaAatttcagt
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7507 3.20e+03 CCGCTC
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7664 2.40e+02 AAAAGCT.Taa
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7665 2.10e+03 aagcttAacAgaatCgaTcgCTTc
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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 Cj1643

Cj1643 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
protein binding go/ molecular_function
Module neighborhood information for Cj1643

Cj1643 has total of 49 gene neighbors in modules 62, 141
Gene neighbors (49)
Gene Common Name Description Module membership
Cj0015c Cj0015c hypothetical protein Cj0015c (NCBI ptt file) 39, 62
Cj0023 purB adenylosuccinate lyase (NCBI ptt file) 62, 146
Cj0024 nrdA ribonucleoside-diphosphate reductase alpha chain (NCBI ptt file) 41, 62
Cj0031 Cj0031 putative type IIS restriction/modification enzyme (NCBI) 106, 141
Cj0124c Cj0124c putative membrane protein (NCBI ptt file) 23, 141
Cj0131 Cj0131 putative periplasmic protein (NCBI ptt file) 49, 62
Cj0149c hom homoserine dehydrogenase (NCBI ptt file) 62, 165
Cj0159c Cj0159c hypothetical protein Cj0159c (NCBI ptt file) 141, 149
Cj0189c Cj0189c hypothetical protein Cj0189c (NCBI ptt file) 76, 141
Cj0299 Cj0299 putative periplasmic beta-lactamase (NCBI ptt file) 19, 62
Cj0319 fliG flagellar motor switch protein (NCBI ptt file) 62, 156
Cj0320 fliH putative flagellar assembly protein (NCBI ptt file) 99, 141
Cj0431 Cj0431 putative periplasmic ATP /GTP-binding protein (NCBI ptt file) 57, 62
Cj0546 Cj0546 hypothetical protein Cj0546 (NCBI ptt file) 23, 62
Cj0647 Cj0647 hypothetical protein Cj0647 (NCBI ptt file) 141, 151
Cj0693c Cj0693c hypothetical protein Cj0693c (NCBI ptt file) 15, 62
Cj0701 Cj0701 putative protease (NCBI ptt file) 110, 141
Cj0702 purE phosphoribosylaminoimidazole carboxylase catalytic subunit (NCBI ptt file) 83, 141
Cj0703 Cj0703 hypothetical protein Cj0703 (NCBI ptt file) 14, 141
Cj0706 Cj0706 hypothetical protein Cj0706 (NCBI ptt file) 62, 102
Cj0707 kdtA 3-deoxy-D-manno-octulosonic-acid transferase (NCBI ptt file) 141, 149
Cj0708 Cj0708 putative ribosomal pseudouridine synthase (NCBI ptt file) 55, 141
Cj0766c tmk putative thymidylate kinase (NCBI ptt file) 39, 62
Cj0770c Cj0770c putative periplasmic protein (NCBI ptt file) 94, 141
Cj0811 lpxK putative tetraacyldisaccharide 4'-kinase (NCBI ptt file) 11, 141
Cj0825 Cj0825 putative processing peptidase (NCBI ptt file) 104, 141
Cj0828c ilvA threonine dehydratase biosynthetic (NCBI ptt file) 54, 62
Cj0957c Cj0957c hypothetical protein Cj0957c (NCBI ptt file) 141, 142
Cj0973 Cj0973 hypothetical protein Cj0973 (NCBI ptt file) 7, 141
Cj0974 Cj0974 very hypothetical protein Cj0974 (NCBI ptt file) 29, 62
Cj1001 rpoD RNA polymerase sigma factor (sigma-70) (NCBI ptt file) 53, 62
Cj1034c Cj1034c possible dnaJ-like protein (NCBI ptt file) 62, 67
Cj1129c wlaC putative glycosyltransferase (NCBI ptt file) 38, 62
Cj1130c wlaB ABC-type transport protein (NCBI ptt file) 62, 141
Cj1180c Cj1180c putative ABC transporter ATP binding protein (NCBI ptt file) 26, 62
Cj1215 Cj1215 putative periplasmic protein (NCBI ptt file) 62, 147
Cj1246c uvrC excinuclease ABC subunit C (NCBI ptt file) 12, 141
Cj1282 mrdB RodA protein homolog (NCBI ptt file) 26, 141
Cj1303 fabH2 putative 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) 106, 141
Cj1371 Cj1371 putative periplasmic protein (vacJ homolog) (NCBI ptt file) 48, 62
Cj1415c cysC possible adenylylsulfate kinase (NCBI ptt file) 109, 141
Cj1440c Cj1440c putative sugar transferase (NCBI ptt file) 128, 141
Cj1471c Cj1471c putative type II protein secretion system E protein (NCBI ptt file) 62, 155
Cj1589 Cj1589 hypothetical protein Cj1589 (NCBI ptt file) 141, 146
Cj1600 hisH amidotransferase HisH (NCBI ptt file) 133, 141
Cj1611 rpsT 30S ribosomal protein S20 (NCBI ptt file) 14, 141
Cj1643 Cj1643 putative periplasmic protein (NCBI ptt file) 62, 141
Cj1670c Cj1670c putative periplasmic protein (NCBI ptt file) 128, 141
Cj1709c Cj1709c putative ribosomal pseudouridine synthase (NCBI ptt file) 128, 141
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 Cj1643
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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