Organism : Campylobacter jejuni | Module List :
Cj1000

putative transcriptional regulator (lysR family) (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1000
(Mouseover regulator name to see its description)

Cj1000 is regulated by 3 influences and regulates 6 modules.
Regulators for Cj1000 (3)
Regulator Module Operator
Cj1000 63 tf
Cj1001 63 tf
Cj1349c 63 tf

Warning: Cj1000 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
7470 1.10e+00 TataAAgaTaTTTAAgc.aAAA
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7471 1.20e-02 caaAAaTTTccTTatAAttTctcG
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7508 1.20e+03 GGCACaCc
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7509 5.10e+03 CaCCgCc
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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 Cj1000

Cj1000 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for Cj1000

Cj1000 has total of 45 gene neighbors in modules 44, 63
Gene neighbors (45)
Gene Common Name Description Module membership
Cj0078c cdtB cytolethal distending toxin (NCBI ptt file) 44, 95
Cj0079c cdtA cytolethal distending toxin (NCBI ptt file) 44, 95
Cj0080 Cj0080 putative membrane protein (NCBI ptt file) 44, 60
Cj0081 cydA cytochrome bd oxidase subunit I (NCBI ptt file) 44, 151
Cj0082 cydB cytochrome bd oxidase subunit II (NCBI ptt file) 44, 128
Cj0164c ubiA putative 4-hydroxybenzoate octaprenyltransferase (NCBI ptt file) 63, 149
Cj0202c Cj0202c hypothetical protein Cj0202c (NCBI ptt file) 63, 155
Cj0271 Cj0271 bacterioferritin comigratory protein homolog (NCBI ptt file) 52, 63
Cj0336c motB putative flagellar motor protein (NCBI ptt file) 44, 123
Cj0338c polA DNA polymerase I (NCBI ptt file) 39, 44
Cj0339 Cj0339 putative transmembrane transport protein (NCBI ptt file) 44, 78
Cj0387 aroK shikimate kinase (NCBI ptt file) 6, 63
Cj0388 trpS tryptophanyl-tRNA synthetase (NCBI ptt file) 63, 166
Cj0444 Cj0444 None 63, 107
Cj0644 Cj0644 hypothetical protein Cj0644 (NCBI ptt file) 44, 165
Cj0646 Cj0646 putative lipoprotein (NCBI ptt file) 19, 63
Cj0730 Cj0730 putative ABC transport system permease (NCBI ptt file) 63, 164
Cj0763c cysE serine acetyltransferase (NCBI ptt file) 44, 45
Cj0854c Cj0854c putative periplasmic protein (NCBI ptt file) 63, 120
Cj0877c Cj0877c very hypothetical protein Cj0877c (NCBI ptt file) 44, 58
Cj0891c serA D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 63, 148
Cj1000 Cj1000 putative transcriptional regulator (lysR family) (NCBI ptt file) 44, 63
Cj1030c lepA lepA GTP-binding protein homolog (NCBI ptt file) 63, 160
Cj1039 murG putative UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 44, 116
Cj1086c Cj1086c hypothetical protein Cj1086c (NCBI ptt file) 63, 81
Cj1146c waaV putative glucosyltransferase (NCBI ptt file) 63, 149
Cj1316c Cj1316c hypothetical protein Cj1316c (NCBI ptt file) 63, 144
Cj1327 neuB2 N-acetylneuraminic acid synthetase (NCBI ptt file) 63, 117
Cj1331 ptmB acylneuraminate cytidylyltransferase (flagellin modification) (NCBI ptt file) 63, 146
Cj1332 ptmA putative oxidoreductase (flagellin modification) (NCBI ptt file) 63, 77
Cj1333 Cj1333 hypothetical protein Cj1333 (1318 family) (NCBI ptt file) 63, 109
Cj1379 selB putative selenocysteine-specific elongation factor (NCBI ptt file) 44, 81
Cj1434c Cj1434c putative sugar transferase (NCBI ptt file) 41, 44
Cj1458c thiL putative thiamin-monophosphate kinase (NCBI ptt file) 44, 63
Cj1459 Cj1459 hypothetical protein Cj1459 (NCBI ptt file) 44, 132
Cj1460 Cj1460 hypothetical protein Cj1460 (NCBI ptt file) 37, 44
Cj1461 Cj1461 possible DNA methylase (NCBI ptt file) 27, 44
Cj1483c Cj1483c putative lipoprotein (NCBI ptt file) 26, 44
Cj1530 Cj1530 putative ATP/GTP-binding protein (NCBI ptt file) 44, 132
Cj1544c Cj1544c putative integral membrane protein (NCBI ptt file) 41, 44
Cj1562 Cj1562 hypothetical protein Cj1562 (NCBI ptt file) 19, 63
Cj1634c aroC chorismate synthase (NCBI ptt file) 63, 110
Cj1641 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diami ligase (NCBI ptt file) 18, 44
Cj1687 Cj1687 putative efflux protein (NCBI ptt file) 44, 54
Cj1727c metY putative O-acetylhomoserine (thiol)-lyase (NCBI ptt file) 63, 83
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 Cj1000
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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