Organism : Campylobacter jejuni | Module List :
Cj1595 rpoA

DNA-directed RNA polymerase alpha chain (NCBI ptt file)

CircVis
Functional Annotations (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 kD subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1595
(Mouseover regulator name to see its description)

Cj1595 is regulated by 6 influences and regulates 7 modules.
Regulators for Cj1595 rpoA (6)
Regulator Module Operator
Cj0473 14 tf
Cj0479 14 tf
Cj0480c 14 tf
Cj1595 14 tf
Cj0473 30 tf
Cj1595 30 tf

Warning: Cj1595 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
7410 4.70e+03 GcTacaACcaTAaAGCaCCG
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7411 1.60e+02 AGtaAAAttaagttAAAAttg
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7442 4.70e+00 GTgtAGCgCagtCTgG
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7443 8.10e+01 GATAaAatatttgCTTt
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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 Cj1595

Cj1595 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
DNA-directed RNA polymerase, alpha subunit/40 kD subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
protein dimerization activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoA tigr/ tigrfam
Module neighborhood information for Cj1595

Cj1595 has total of 52 gene neighbors in modules 14, 30
Gene neighbors (52)
Gene Common Name Description Module membership
Cj0094 rplU 50S ribosomal protein L21 (NCBI ptt file) 14, 111
Cj0095 rpmA 50S ribosomal protein L27 (NCBI ptt file) 14, 83
Cj0129c Cj0129c outer membrane protein (NCBI ptt file) 14, 133
Cj0154c Cj0154c putative methylase (NCBI ptt file) 14, 151
Cj0155c rpmE 50S ribosomal protein L31 (NCBI ptt file) 14, 123
Cj0274 lpxA acyl-[acyl-carrier-protein]--UDP-N-acetylglucosam O-acyltransferase (NCBI ptt file) 14, 61
Cj0275 clpX ATP-dependent clp protease ATP-binding subunit clpX (NCBI ptt file) 14, 151
Cj0311 Cj0311 ctc protein homolog (NCBI ptt file) 30, 95
Cj0330c rpmF 50S ribosomal protein L32 (NCBI ptt file) 14, 151
Cj0443 accA acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (NCBI ptt file) 14, 26
Cj0470 tuf elongation factor TU (NCBI ptt file) 9, 30
Cj0471 rpmG 50S ribosomal protein L33 (NCBI ptt file) 9, 30
Cj0472 secE preprotein translocase SecE subunit (NCBI ptt file) 14, 163
Cj0473 nusG putative transcription antitermination protein (NCBI ptt file) 14, 163
Cj0474 rplK 50S ribosomal protein L11 (NCBI ptt file) 14, 163
Cj0475 rplA 50S ribosomal protein L1 (NCBI ptt file) 14, 163
Cj0476 rplJ 50S ribosomal protein L10 (NCBI ptt file) 14, 163
Cj0477 rplL 50S ribosomal protein L7 /L12 (NCBI ptt file) 14, 42
Cj0491 rpsL 30S ribosomal protein S12 (NCBI ptt file) 30, 83
Cj0492 rpsG 30S ribosomal protein S7 (NCBI ptt file) 30, 163
Cj0694 Cj0694 putative periplasmic protein (NCBI ptt file) 14, 118
Cj0703 Cj0703 hypothetical protein Cj0703 (NCBI ptt file) 14, 141
Cj0900c Cj0900c small hydrophobic protein (NCBI ptt file) 14, 66
Cj1092c secF protein-export membrane protein (NCBI ptt file) 14, 111
Cj1093c secD protein-export membrane protein (NCBI ptt file) 14, 133
Cj1106 Cj1106 possible periplasmic thioredoxin (NCBI ptt file) 14, 98
Cj1181c tsf elongation factor TS (NCBI ptt file) 30, 160
Cj1182c rpsB 30S ribosomal protein S2 (NCBI ptt file) 9, 30
Cj1280c Cj1280c putative ribosomal pseudouridine synthase (NCBI ptt file) 14, 97
Cj1407c Cj1407c putative phospho-sugar mutase (NCBI ptt file) 14, 111
Cj1441c kfiD putative UDP-glucose 6-dehydrogenase (NCBI ptt file) 14, 137
Cj1480c rplM 50S ribosomal protein L13 (NCBI ptt file) 4, 30
Cj1495c Cj1495c hypothetical protein Cj1495c (NCBI ptt file) 14, 98
Cj1540 Cj1540 putative periplasmic protein (NCBI ptt file) 14, 123
Cj1591 rpmJ 50S ribosomal protein L36 (NCBI ptt file) 9, 30
Cj1592 rpsM 30S ribosomal protein S13 (NCBI ptt file) 30, 163
Cj1593 rpsK 30S ribosomal protein S11 (NCBI ptt file) 30, 163
Cj1594 rpsD 30S ribosomal protein S4 (NCBI ptt file) 30, 163
Cj1595 rpoA DNA-directed RNA polymerase alpha chain (NCBI ptt file) 14, 30
Cj1611 rpsT 30S ribosomal protein S20 (NCBI ptt file) 14, 141
Cj1693c rpsH 30S ribosomal protein S8 (NCBI ptt file) 4, 30
Cj1694c rpsN 30S ribosomal protein S14 (NCBI ptt file) 4, 30
Cj1696c rplX 50S ribosomal protein L24 (NCBI ptt file) 14, 163
Cj1697c rplN 50S ribosomal protein L14 (NCBI ptt file) 4, 30
Cj1702c rplV 50S ribosomal protein L22 (NCBI ptt file) 4, 30
Cj1706c rplD 50S ribosomal protein L4 (NCBI ptt file) 4, 30
Cj1707c rplC 50S ribosomal protein L3 (NCBI ptt file) 4, 30
Cj1708c rpsJ 30S ribosomal protein S10 (NCBI ptt file) 30, 163
Cjp09 tRNA-Trp tRNA-Trp (NCBI) 30, 73
Cjp33 tRNA-Pro tRNA-Pro (NCBI) 30, 107
Cjt3 tRNA-Arg tRNA-Arg (NCBI) 30, 73
Cjt4 tRNA-Arg tRNA-Arg (NCBI) 30, 105
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 Cj1595
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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