Organism : Campylobacter jejuni | Module List :
Cj0335 flhB

flagellar biosynthetic protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Flagellar biosynthesis pathway, component FlhB cog/ cog
protein secretion go/ biological_process
membrane go/ cellular_component
Flagellar assembly kegg/ kegg pathway
flhB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0335
(Mouseover regulator name to see its description)

Cj0335 is regulated by 2 influences and regulates 0 modules.
Regulators for Cj0335 flhB (2)
Regulator Module Operator
Cj0480c 129 tf
Cj0670 129 tf

Warning: Cj0335 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
7594 9.00e+00 aaggaaaAaTataGc
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7595 2.70e+03 cCagttGAagCcAtT
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7640 7.10e+03 CGGCAaCc
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7641 4.00e+03 cggcTtaAGT
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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 Cj0335

Cj0335 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Flagellar biosynthesis pathway, component FlhB cog/ cog
protein secretion go/ biological_process
membrane go/ cellular_component
Flagellar assembly kegg/ kegg pathway
flhB tigr/ tigrfam
Module neighborhood information for Cj0335

Cj0335 has total of 41 gene neighbors in modules 106, 129
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0031 Cj0031 putative type IIS restriction/modification enzyme (NCBI) 106, 141
Cj0293 surE SurE protein homolog (NCBI ptt file) 17, 129
Cj0335 flhB flagellar biosynthetic protein (NCBI ptt file) 106, 129
Cj0380c Cj0380c hypothetical protein Cj0380c (NCBI ptt file) 1, 129
Cj0386 Cj0386 putative GTP-binding protein (NCBI ptt file) 36, 106
Cj0397c Cj0397c hypothetical protein Cj0397c (NCBI ptt file) 35, 129
Cj0421c Cj0421c putative integral membrane protein (NCBI ptt file) 129, 155
Cj0464 recG ATP-dependent DNA helicase (NCBI ptt file) 12, 106
Cj0499 Cj0499 HIT-like protein (NCBI ptt file) 106, 133
Cj0500 Cj0500 putative ATP /GTP binding protein (NCBI ptt file) 51, 106
Cj0510c Cj0510c hypothetical protein Cj0510c (NCBI ptt file) 41, 129
Cj0569 Cj0569 hypothetical protein Cj0569 (NCBI ptt file) 51, 106
Cj0618 Cj0618 hypothetical protein Cj0618 (617 family) (NCBI ptt file) 77, 129
Cj0634 Cj0634 SMF family protein (NCBI ptt file) 106, 109
Cj0660c Cj0660c putative transmembrane protein (NCBI ptt file) 15, 129
Cj0670 rpoN RNA polymerase sigma-54 factor (NCBI ptt file) 129, 155
Cj0739 Cj0739 hypothetical protein Cj0739 (NCBI ptt file) 106, 116
Cj0790 purU formyltetrahydrofolate deformylase (NCBI ptt file) 72, 129
Cj0798c ddlA putative D-alanine--D-alanine ligase (NCBI ptt file) 129, 155
Cj0799c ruvA putative Holliday junction DNA helicase (NCBI ptt file) 46, 129
Cj0816 Cj0816 hypothetical protein Cj0816 (NCBI ptt file) 129, 167
Cj0850c Cj0850c transmembrane transport protein (NCBI ptt file) 72, 129
Cj0979c Cj0979c putative secreted nuclease (NCBI ptt file) 67, 129
Cj1043c Cj1043c possible transferase (NCBI ptt file) 43, 106
Cj1047c Cj1047c hypothetical protein Cj1047c (NCBI ptt file) 43, 106
Cj1048c dapE succinyl-diaminopimelate desuccinylase (NCBI ptt file) 51, 106
Cj1073c lon ATP-dependent protease La (NCBI ptt file) 129, 165
Cj1125c wlaG putative galactosyltransferase (NCBI ptt file) 106, 109
Cj1179c fliR flagellar biosynthetic protein (NCBI ptt file) 116, 129
Cj1194 Cj1194 possible phosphate permease (NCBI ptt file) 26, 129
Cj1236 Cj1236 hypothetical protein Cj1236 (NCBI ptt file) 72, 106
Cj1254 Cj1254 hypothetical protein Cj1254 (NCBI ptt file) 23, 106
Cj1263 recR recombination protein (NCBI ptt file) 70, 106
Cj1303 fabH2 putative 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) 106, 141
Cj1343c Cj1343c putative periplasmic protein (NCBI ptt file) 92, 106
Cj1353 ceuC enterochelin uptake permease (NCBI ptt file) 3, 106
Cj1398 feoB ferrous iron transport protein (NCBI ptt file) 55, 129
Cj1517 moaD possible molybdopterin converting factor, subunit 1 (NCBI ptt file) 98, 106
Cj1519 moeA2 putative molybdopterin biosynthesis protein (NCBI ptt file) 80, 106
Cj1547 Cj1547 homolog of BLC protein (NCBI ptt file) 129, 167
Cj1667c Cj1667c repA protein homolog (NCBI ptt file) 106, 129
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 Cj0335
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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