Organism : Campylobacter jejuni | Module List :
Cj1622 ribD

putative riboflavin-specific deaminase (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
eubact_ribD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1622
(Mouseover regulator name to see its description)

Cj1622 is regulated by 1 influences and regulates 0 modules.
Regulators for Cj1622 ribD (1)
Regulator Module Operator
Cj0670 37 tf

Warning: Cj1622 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
7456 4.70e+04 CCGtAG
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7457 1.70e+04 CAGcTTtTGGtcc
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7680 2.20e-02 TcGCcAAActatgggatatG
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7681 6.20e+02 CAAcCcCGaGTG
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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 Cj1622

Cj1622 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
eubact_ribD tigr/ tigrfam
Module neighborhood information for Cj1622

Cj1622 has total of 37 gene neighbors in modules 37, 149
Gene neighbors (37)
Gene Common Name Description Module membership
Cj0004c Cj0004c putative periplasmic protein (NCBI ptt file) 37, 57
Cj0022c Cj0022c putative ribosomal pseudouridine synthase (NCBI ptt file) 139, 149
Cj0055c Cj0055c hypothetical protein Cj0055c (NCBI ptt file) 110, 149
Cj0062c Cj0062c putative integral membrane protein (NCBI ptt file) 116, 149
Cj0156c Cj0156c hypothetical protein Cj0156c (NCBI ptt file) 149, 161
Cj0158c Cj0158c putative haem-binding lipoprotein (NCBI ptt file) 68, 149
Cj0159c Cj0159c hypothetical protein Cj0159c (NCBI ptt file) 141, 149
Cj0160c Cj0160c hypothetical protein Cj0160c (NCBI ptt file) 41, 149
Cj0164c ubiA putative 4-hydroxybenzoate octaprenyltransferase (NCBI ptt file) 63, 149
Cj0247c Cj0247c hypothetical protein Cj0247c (NCBI ptt file) 37, 51
Cj0321 dxs 1-deoxyxylulose-5-phosphate synthase (NCBI ptt file) 70, 149
Cj0340 Cj0340 putative nucleoside hydrolase (NCBI ptt file) 19, 37
Cj0407 lgt prolipoprotein diacylglyceryl transferase (NCBI ptt file) 37, 162
Cj0454c Cj0454c putative membrane protein (NCBI ptt file) 37, 81
Cj0576 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (NCBI ptt file) 37, 110
Cj0707 kdtA 3-deoxy-D-manno-octulosonic-acid transferase (NCBI ptt file) 141, 149
Cj0727 Cj0727 putative periplasmic solute-binding protein (NCBI ptt file) 37, 55
Cj0732 Cj0732 ABC transport system ATP-binding protein (NCBI ptt file) 37, 152
Cj0733 Cj0733 hypothetical protein Cj0733 (NCBI ptt file) 15, 37
Cj0735 Cj0735 putative periplasmic protein (NCBI ptt file) 37, 116
Cj0849c Cj0849c hypothetical protein Cj0849c (NCBI ptt file) 23, 37
Cj0945c Cj0945c putative helicase (NCBI ptt file) 37, 58
Cj0963 Cj0963 hypothetical protein Cj0963 (NCBI ptt file) 37, 60
Cj1002c Cj1002c hypothetical protein Cj1002c (NCBI ptt file) 37, 81
Cj1097 Cj1097 putative transmembrane transport protein (NCBI ptt file) 37, 60
Cj1138 Cj1138 putative galactosyltransferase (NCBI ptt file) 37, 108
Cj1146c waaV putative glucosyltransferase (NCBI ptt file) 63, 149
Cj1166c Cj1166c putative integral membrane protein (NCBI ptt file) 122, 149
Cj1222c Cj1222c putative two-component sensor (NCBI ptt file) 20, 149
Cj1235 Cj1235 putative periplasmic protein (NCBI ptt file) 40, 149
Cj1344c Cj1344c putative glycoprotease (NCBI ptt file) 92, 149
Cj1460 Cj1460 hypothetical protein Cj1460 (NCBI ptt file) 37, 44
Cj1482c Cj1482c hypothetical protein Cj1482c (NCBI ptt file) 23, 37
Cj1551c Cj1551c putative type I restriction enzyme S protein (NCBI ptt file) 37, 75
Cj1608 Cj1608 possible two-component regulator (NCBI ptt file) 149, 154
Cj1622 ribD putative riboflavin-specific deaminase (NCBI ptt file) 37, 149
Cj1713 Cj1713 hypothetical protein Cj1713 (NCBI ptt file) 70, 149
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 Cj1622
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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