Organism : Campylobacter jejuni | Module List :
Cj0641

hypothetical protein Cj0641 (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted sugar kinase cog/ cog
NAD+ kinase activity go/ molecular_function
metabolic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0641
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0641!

Warning: Cj0641 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
7404 5.80e+02 GGcAA.ccT..a.GattGGcAaAA
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7405 8.80e+02 ccCCAAgcggT
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7632 7.30e+00 cccaAgCt
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7633 5.30e+03 GcGGTGGATC
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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 Cj0641

Cj0641 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted sugar kinase cog/ cog
NAD+ kinase activity go/ molecular_function
metabolic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for Cj0641

Cj0641 has total of 39 gene neighbors in modules 11, 125
Gene neighbors (39)
Gene Common Name Description Module membership
Cj0103 atpF ATP synthase F0 sector B subunit (NCBI ptt file) 125, 127
Cj0127c accD acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (NCBI ptt file) 11, 145
Cj0135 Cj0135 hypothetical protein Cj0135 (NCBI ptt file) 95, 125
Cj0136 infB translation initiation factor IF-2 (NCBI ptt file) 38, 125
Cj0137 Cj0137 hypothetical protein Cj0137 (NCBI ptt file) 83, 125
Cj0138 Cj0138 hypothetical protein Cj0138 (NCBI ptt file) 11, 158
Cj0396c Cj0396c putative lipoprotein (NCBI ptt file) 52, 125
Cj0433c mraY phospho-N-acetylmuramoyl-pentapeptide- transferase (NCBI ptt file) 77, 125
Cj0522 Cj0522 putative membrane protein (NCBI ptt file) 23, 125
Cj0532 mdh malate dehydrogenase (NCBI ptt file) 11, 110
Cj0574 ilvI acetolactate synthase large subunit (NCBI ptt file) 11, 110
Cj0625 hypD hydrogenase isoenzymes formation protein (NCBI ptt file) 32, 125
Cj0641 Cj0641 hypothetical protein Cj0641 (NCBI ptt file) 11, 125
Cj0752 Cj0752 None 11, 164
Cj0762c aspB aspartate aminotransferase (NCBI ptt file) 11, 48
Cj0784 Cj0784 putative periplasmic protein (NCBI ptt file) 11, 145
Cj0809c Cj0809c putative hydrolase (NCBI ptt file) 11, 29
Cj0811 lpxK putative tetraacyldisaccharide 4'-kinase (NCBI ptt file) 11, 141
Cj0812 thrC threonine synthase (NCBI ptt file) 11, 81
Cj0813 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase (NCBI ptt file) 11, 103
Cj0894c lytB lytB homolog (NCBI ptt file) 69, 125
Cj0897c pheS phenylalanyl-tRNA synthetase alpha chain (NCBI ptt file) 11, 145
Cj0905c alr alanine racemase (NCBI ptt file) 122, 125
Cj0913c hupB DNA-binding protein HU homolog (NCBI ptt file) 11, 94
Cj1062 Cj1062 hypothetical protein Cj1062 (NCBI ptt file) 11, 57
Cj1127c wlaE putative glycosyltransferase (NCBI ptt file) 109, 125
Cj1309c Cj1309c hypothetical protein Cj1309c (NCBI ptt file) 70, 125
Cj1320 Cj1320 putative aminotransferase (degT family) (NCBI ptt file) 56, 125
Cj1345c Cj1345c putative periplasmic protein (NCBI ptt file) 11, 92
Cj1347c cdsA phosphatidate cytidylyltransferase (NCBI ptt file) 11, 92
Cj1361c Cj1361c hypothetical protein Cj1361c (NCBI ptt file) 6, 11
Cj1367c Cj1367c possible nucleotidyltransferase (NCBI ptt file) 88, 125
Cj1399c hydA2 putative Ni/Fe-hydrogenase small subunit (NCBI ptt file) 41, 125
Cj1436c Cj1436c putative aminotransferase (NCBI ptt file) 88, 125
Cj1437c Cj1437c putative aminotransferase (NCBI ptt file) 26, 125
Cj1454c Cj1454c hypothetical protein Cj1454c (NCBI ptt file) 125, 158
Cj1505c Cj1505c hypothetical protein Cj1505c (NCBI ptt file) 11, 97
Cj1610 pgpA putative phosphatidylglycerophosphatase (NCBI ptt file) 11, 158
Cj1714 Cj1714 small hydrophobic protein (NCBI ptt file) 11, 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 Cj0641
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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