Organism : Campylobacter jejuni | Module List :
Cj1253 pnp

polyribonucleotide nucleotidyltransferase (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) cog/ cog
3'-5'-exoribonuclease activity go/ molecular_function
RNA binding go/ molecular_function
polyribonucleotide nucleotidyltransferase activity go/ molecular_function
RNA processing go/ biological_process
mRNA catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
polynuc_phos tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1253
(Mouseover regulator name to see its description)

Cj1253 is regulated by 2 influences and regulates 2 modules.
Regulators for Cj1253 pnp (2)
Regulator Module Operator
Cj1253 145 tf
Cj1533c 145 tf

Warning: Cj1253 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
7490 3.50e+03 CCcTCC
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7491 7.00e+04 CTTcGGaaTTTGC
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7672 6.50e-04 gCaaggGcgtAgga
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7673 5.60e+00 CTt..aaAAAA.GcA
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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 Cj1253

Cj1253 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) cog/ cog
3'-5'-exoribonuclease activity go/ molecular_function
RNA binding go/ molecular_function
polyribonucleotide nucleotidyltransferase activity go/ molecular_function
RNA processing go/ biological_process
mRNA catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
polynuc_phos tigr/ tigrfam
Module neighborhood information for Cj1253

Cj1253 has total of 39 gene neighbors in modules 54, 145
Gene neighbors (39)
Gene Common Name Description Module membership
Cj0006 Cj0006 putative integral membrane protein (NCBI ptt file) 12, 54
Cj0044c Cj0044c hypothetical protein Cj0044c (NCBI ptt file) 42, 145
Cj0127c accD acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (NCBI ptt file) 11, 145
Cj0133 Cj0133 hypothetical protein Cj0133 (NCBI ptt file) 54, 117
Cj0141c Cj0141c ABC transporter integral membrane protein (NCBI ptt file) 52, 54
Cj0148c Cj0148c hypothetical protein Cj0148c (NCBI ptt file) 8, 54
Cj0196c purF amidophosphoribosyltransferase (NCBI ptt file) 83, 145
Cj0348 trpB tryptophan synthase beta chain (NCBI ptt file) 45, 145
Cj0389 serS seryl-tRNA synthetase (NCBI ptt file) 145, 159
Cj0435 fabG 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 42, 145
Cj0586 ligA DNA ligase (NCBI ptt file) 26, 145
Cj0589 ribF putative riboflavin kinase /FMN adenylyltransferase (NCBI ptt file) 104, 145
Cj0607 Cj0607 ABC-type transmembrane transport protein (NCBI ptt file) 145, 158
Cj0627 hypA hydrogenase expression /formation protein (NCBI ptt file) 45, 145
Cj0645 Cj0645 putative secreted transglycosylase (NCBI ptt file) 81, 145
Cj0669 Cj0669 ABC-transporter ATP-binding protein (NCBI ptt file) 61, 145
Cj0679 kdpD' truncated KdpD protein (NCBI ptt file) 17, 54
Cj0784 Cj0784 putative periplasmic protein (NCBI ptt file) 11, 145
Cj0828c ilvA threonine dehydratase biosynthetic (NCBI ptt file) 54, 62
Cj0829c Cj0829c hypothetical protein Cj0829c (NCBI ptt file) 48, 54
Cj0836 ogt methylated-DNA--protein-cysteine methyltransferase (NCBI ptt file) 45, 145
Cj0853c hemL glutamate-1-semialdehyde 2,1-aminomutase (NCBI ptt file) 80, 145
Cj0873c Cj0873c hypothetical protein Cj0873c (NCBI ptt file) 97, 145
Cj0897c pheS phenylalanyl-tRNA synthetase alpha chain (NCBI ptt file) 11, 145
Cj1023c asd aspartate-semialdehyde dehydrogenase (NCBI ptt file) 54, 159
Cj1210 Cj1210 putative integral membrane protein (NCBI ptt file) 26, 54
Cj1253 pnp polyribonucleotide nucleotidyltransferase (NCBI ptt file) 54, 145
Cj1257c Cj1257c putative efflux pump (NCBI ptt file) 145, 158
Cj1276c Cj1276c putative integral membrane protein (NCBI ptt file) 48, 54
Cj1286c upp uracil phosphoribosyltransferase (NCBI ptt file) 52, 145
Cj1355 ceuE enterochelin uptake periplasmic binding protein (NCBI ptt file) 3, 145
Cj1393 metC' putative cystathionine beta-lyase (RefSeq) 108, 145
Cj1406c Cj1406c putative periplasmic protein (NCBI ptt file) 45, 145
Cj1449c Cj1449c hypothetical protein Cj1449c (NCBI ptt file) 54, 57
Cj1570c nuoJ NADH dehydrogenase I chain J (NCBI ptt file) 42, 54
Cj1607 Cj1607 hypothetical protein Cj1607 (NCBI ptt file) 54, 158
Cj1665 Cj1665 possible lipoprotein thiredoxin (NCBI ptt file) 145, 156
Cj1680c Cj1680c putative periplasmic protein (NCBI ptt file) 54, 59
Cj1687 Cj1687 putative efflux protein (NCBI ptt file) 44, 54
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 Cj1253
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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