Organism : Campylobacter jejuni | Module List :
Cj0061c fliA

putative RNA polymerase sigma factor for flagellar operon (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0061c
(Mouseover regulator name to see its description)

Cj0061c is regulated by 6 influences and regulates 3 modules.
Regulators for Cj0061c fliA (6)
Regulator Module Operator
Cj0061c 68 tf
Cj0480c 68 tf
Cj1050c 68 tf
Cj1230 68 tf
Cj1533c 68 tf
Cj1552c 68 tf

Warning: Cj0061c 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
7518 3.30e+03 CAAGGA.A
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7519 1.60e+03 tgtaGCttGGgtTt
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7660 4.50e+02 ccccCTcCCC
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7661 9.70e+02 CGCTAATCTTCCAAAGTG
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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 Cj0061c

Cj0061c is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
FliA_WhiG tigr/ tigrfam
Module neighborhood information for Cj0061c

Cj0061c has total of 36 gene neighbors in modules 68, 139
Gene neighbors (36)
Gene Common Name Description Module membership
Cj0022c Cj0022c putative ribosomal pseudouridine synthase (NCBI ptt file) 139, 149
Cj0026c Cj0026c hypothetical protein Cj0026c (NCBI ptt file) 50, 68
Cj0053c trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI ptt file) 26, 139
Cj0061c fliA putative RNA polymerase sigma factor for flagellar operon (NCBI ptt file) 68, 139
Cj0126c Cj0126c hypothetical protein Cj0126c (NCBI ptt file) 17, 68
Cj0158c Cj0158c putative haem-binding lipoprotein (NCBI ptt file) 68, 149
Cj0200c Cj0200c putative periplasmic protein (NCBI ptt file) 68, 86
Cj0277 Cj0277 putative periplasmic protein (NCBI ptt file) 46, 68
Cj0344 Cj0344 hypothetical protein Cj0344 (NCBI ptt file) 68, 121
Cj0364 Cj0364 hypothetical protein Cj0364 (NCBI ptt file) 49, 68
Cj0462 Cj0462 hypothetical protein Cj0462 (NCBI ptt file) 68, 157
Cj0617 Cj0617 hypothetical protein Cj0617 (617 family) (NCBI ptt file) 23, 68
Cj0764c speA biosynthetic arginine decarboxylase (NCBI ptt file) 68, 89
Cj0858c murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 68, 98
Cj0965c Cj0965c hypothetical protein Cj0965c (NCBI ptt file) 139, 160
Cj1038 Cj1038 probable cell division/peptidoglycan biosynthesis protein (NCBI ptt file) 116, 139
Cj1087c Cj1087c putative periplasmic protein (NCBI ptt file) 68, 118
Cj1155c Cj1155c putative cation-transporting ATPase (NCBI ptt file) 46, 68
Cj1172c Cj1172c hypothetical protein Cj1172c (NCBI ptt file) 68, 123
Cj1213c glcD putative glycolate oxidase subunit D (NCBI ptt file) 49, 68
Cj1259 porA major outer membrane protein (NCBI ptt file) 68, 121
Cj1261 racR two-component regulator (NCBI ptt file) 20, 68
Cj1314c Cj1314c putative cyclase (NCBI ptt file) 139, 155
Cj1318 Cj1318 hypothetical protein Cj1318 (1318 family) (NCBI ptt file) 112, 139
Cj1319 Cj1319 putative nucleotide sugar dehydratase (NCBI ptt file) 109, 139
Cj1339c flaA flagellin (NCBI ptt file) 20, 68
Cj1368 Cj1368 hypothetical protein Cj1368 (NCBI ptt file) 68, 121
Cj1496c Cj1496c putative periplasmic protein (NCBI ptt file) 139, 156
Cj1497c Cj1497c hypothetical protein Cj1497c (NCBI ptt file) 139, 156
Cj1500 Cj1500 putative integral membrane protein (NCBI ptt file) 139, 156
Cj1501 Cj1501 hypothetical protein Cj1501 (NCBI ptt file) 139, 156
Cj1515c Cj1515c putative decarboxylase (NCBI ptt file) 139, 161
Cj1555c Cj1555c hypothetical protein Cj1555c (NCBI ptt file) 31, 68
Cj1605c dapD possible 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI ptt file) 49, 68
Cj1623 Cj1623 putative membrane protein (NCBI ptt file) 15, 139
Cjr06 Cjr06 5S ribosomal RNA (NCBI) 49, 68
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 Cj0061c
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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