Organism : Campylobacter jejuni | Module List :
Cj1072 rpsR

30S ribosomal protein S18 (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Ribosomal protein S18 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
S18 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1072
(Mouseover regulator name to see its description)

Cj1072 is regulated by 8 influences and regulates 0 modules.
Regulators for Cj1072 rpsR (8)
Regulator Module Operator
Cj0287c 52 tf
Cj0382c 52 tf
Cj0400 52 tf
Cj0479 52 tf
Cj0480c 52 tf
Cj0571 52 tf
Cj0400 138 tf
Cj0670 138 tf

Warning: Cj1072 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
7486 1.90e+01 TtgGCttaTGGA
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7487 5.20e+04 GtgtTTGcaGtAGaaAtaga
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7658 7.20e+02 GGCACACC
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7659 8.80e+03 AtCaAGaG
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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 Cj1072

Cj1072 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribosomal protein S18 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
S18 tigr/ tigrfam
Module neighborhood information for Cj1072

Cj1072 has total of 46 gene neighbors in modules 52, 138
Gene neighbors (46)
Gene Common Name Description Module membership
Cj0141c Cj0141c ABC transporter integral membrane protein (NCBI ptt file) 52, 54
Cj0157c Cj0157c putative integral membrane protein (NCBI ptt file) 52, 118
Cj0191c def polypeptide deformylase (NCBI ptt file) 52, 118
Cj0229 Cj0229 putative acetyltransferase (NCBI ptt file) 90, 138
Cj0231c nrdB ribonucleoside-diphosphate reductase beta chain (NCBI ptt file) 133, 138
Cj0233c pyrE putative orotate phosphoribosyltransferase (NCBI ptt file) 138, 156
Cj0235c secG putative protein-export membrane protein (NCBI ptt file) 132, 138
Cj0244 rpmI 50s ribosomal protein L35 (NCBI ptt file) 138, 151
Cj0271 Cj0271 bacterioferritin comigratory protein homolog (NCBI ptt file) 52, 63
Cj0309c Cj0309c putative efflux protein (NCBI ptt file) 52, 95
Cj0315 Cj0315 hypothetical protein Cj0315 (NCBI ptt file) 52, 151
Cj0326 serC phosphoserine aminotransferase (NCBI ptt file) 41, 138
Cj0327 Cj0327 hypothetical protein Cj0327 (NCBI ptt file) 118, 138
Cj0361 lspA lipoprotein signal peptidase (NCBI ptt file) 52, 165
Cj0382c nusB transcription termination protein (NCBI ptt file) 52, 56
Cj0396c Cj0396c putative lipoprotein (NCBI ptt file) 52, 125
Cj0479 rpoC DNA-directed RNA polymerase beta' chain (NCBI ptt file) 52, 90
Cj0493 fusA elongation factor G (NCBI ptt file) 52, 132
Cj0517 crcB CRCB protein homolog (NCBI ptt file) 47, 138
Cj0578c mttB sec-independant protein translocase (NCBI ptt file) 3, 138
Cj0608 Cj0608 putative outer membrane protein (NCBI ptt file) 88, 138
Cj0773c Cj0773c binding-protein dependent transport system permease protein (NCBI ptt file) 52, 59
Cj0845c gltX glutamyl-tRNA synthetase (NCBI ptt file) 18, 138
Cj0874c Cj0874c cytochrome C (NCBI ptt file) 52, 154
Cj0914c Cj0914c CiaB protein (NCBI ptt file) 3, 52
Cj1071 ssb single-strand DNA binding protein (NCBI ptt file) 9, 138
Cj1072 rpsR 30S ribosomal protein S18 (NCBI ptt file) 52, 138
Cj1105 smpB small protein B homolog (NCBI ptt file) 18, 138
Cj1115c Cj1115c putative membrane protein (NCBI ptt file) 52, 150
Cj1128c wlaD putative glycosyltransferase (NCBI ptt file) 118, 138
Cj1168c Cj1168c putative integral membrane protein (dedA homolog) (NCBI ptt file) 117, 138
Cj1198 Cj1198 hypothetical protein Cj1198 (NCBI ptt file) 52, 111
Cj1243 hemE uroporphyrinogen decarboxylase (NCBI ptt file) 118, 138
Cj1256c Cj1256c putative membrane protein (NCBI ptt file) 26, 52
Cj1267c hydA Ni/Fe-hydrogenase small chain (NCBI ptt file) 52, 170
Cj1271c tyrS tyrosyl-tRNA synthetase (NCBI ptt file) 18, 138
Cj1285c Cj1285c hypothetical protein Cj1285c (NCBI ptt file) 52, 153
Cj1286c upp uracil phosphoribosyltransferase (NCBI ptt file) 52, 145
Cj1287c Cj1287c malate oxidoreductase (NCBI ptt file) 52, 83
Cj1335 maf4 motility accessory factor (function unknown) (NCBI) 138, 166
Cj1485c Cj1485c putative periplasmic protein (NCBI ptt file) 13, 52
Cj1569c nuoK NADH dehydrogenase I chain K (NCBI ptt file) 52, 166
Cj1599 hisB imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file) 98, 138
Cj1604 hisI phosphoribosyl-AMP cyclohydrolase/ phosphoribosyl-ATP pyrophosphohydrolase (NCBI ptt file) 52, 84
Cj1666c Cj1666c putative periplasmic protein (NCBI ptt file) 52, 123
Cj1689c rplO 50S ribosomal protein L15 (NCBI ptt file) 128, 138
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 Cj1072
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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