Organism : Campylobacter jejuni | Module List :
Cj0508 pbpA

penicillin-binding protein (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
Membrane carboxypeptidase (penicillin-binding protein) cog/ cog
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
PBP_1a_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0508
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0508!

Warning: Cj0508 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
7474 1.50e+04 GCcCAAcATCTcGC
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7475 4.10e+04 cGCAaCG
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7558 1.10e+04 CTcaATGGGtGG
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7559 1.80e+04 GAGCcTG
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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 Cj0508

Cj0508 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Membrane carboxypeptidase (penicillin-binding protein) cog/ cog
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
PBP_1a_fam tigr/ tigrfam
Module neighborhood information for Cj0508

Cj0508 has total of 48 gene neighbors in modules 46, 88
Gene neighbors (48)
Gene Common Name Description Module membership
Cj0019c Cj0019c MCP-domain signal transduction protein (NCBI ptt file) 13, 46
Cj0120 Cj0120 hypothetical protein Cj0120 (NCBI ptt file) 88, 150
Cj0187c purN phosphoribosylglycinamide formyltransferase (NCBI ptt file) 46, 117
Cj0246c Cj0246c putative MCP-domain signal transduction protein (NCBI ptt file) 47, 88
Cj0248 Cj0248 hypothetical protein Cj0248 (NCBI ptt file) 47, 88
Cj0254 Cj0254 hypothetical protein Cj0254 (NCBI ptt file) 46, 162
Cj0277 Cj0277 putative periplasmic protein (NCBI ptt file) 46, 68
Cj0347 trpF N-(5'-phosphoribosyl)anthranilate isomerase (NCBI ptt file) 88, 104
Cj0390 Cj0390 putative transmembrane protein (NCBI ptt file) 46, 71
Cj0455c Cj0455c putative membrane protein (NCBI ptt file) 46, 70
Cj0461c Cj0461c putative integral membrane protein (NCBI ptt file) 46, 88
Cj0505c Cj0505c putative aminotransferase (degT family) (NCBI ptt file) 47, 88
Cj0508 pbpA penicillin-binding protein (NCBI ptt file) 46, 88
Cj0541 Cj0541 polyprenyl synthetase (NCBI ptt file) 46, 50
Cj0551 efp elongation factor P (NCBI ptt file) 25, 46
Cj0585 folP putative dihydropteroate synthase (NCBI ptt file) 88, 117
Cj0605 Cj0605 putative amidohydrolase (NCBI ptt file) 88, 161
Cj0608 Cj0608 putative outer membrane protein (NCBI ptt file) 88, 138
Cj0683 Cj0683 putative periplasmic protein (NCBI ptt file) 88, 165
Cj0775c valS valyl-tRNA synthetase (NCBI ptt file) 59, 88
Cj0799c ruvA putative Holliday junction DNA helicase (NCBI ptt file) 46, 129
Cj0880c Cj0880c hypothetical protein Cj0880c (NCBI ptt file) 79, 88
Cj0902 glnQ putative glutamine transport ATP-binding protein (NCBI ptt file) 48, 88
Cj0903c Cj0903c putative amino-acid transport protein (NCBI ptt file) 46, 78
Cj0935c Cj0935c putative transmembrane transport protein (NCBI ptt file) 46, 154
Cj0959c Cj0959c hypothetical protein Cj0959c (NCBI ptt file) 46, 47
Cj0997 Cj0997 gidB homolog (NCBI ptt file) 36, 46
Cj1085c mfd transcription-repair coupling factor (NCBI ptt file) 88, 151
Cj1099 Cj1099 peptidase (M3 family) (NCBI ptt file) 46, 89
Cj1134 htrB putative lipid A biosynthesis lauroyl acyltransferase (NCBI ptt file) 45, 46
Cj1137c Cj1137c hypothetcal protein Cj1137c (NCBI ptt file) 46, 124
Cj1155c Cj1155c putative cation-transporting ATPase (NCBI ptt file) 46, 68
Cj1158c Cj1158c small hydrophobic protein (NCBI ptt file) 46, 58
Cj1311 neuA2 acylneuraminate cytidylyltransferase (NCBI ptt file) 18, 88
Cj1352 ceuB enterochelin uptake permease (NCBI ptt file) 12, 46
Cj1367c Cj1367c possible nucleotidyltransferase (NCBI ptt file) 88, 125
Cj1370 Cj1370 putative nucleotide phosphoribosyltransferase (NCBI ptt file) 36, 46
Cj1372 Cj1372 putative periplasmic protein (NCBI ptt file) 41, 88
Cj1436c Cj1436c putative aminotransferase (NCBI ptt file) 88, 125
Cj1444c kpsD putative capsule polysaccharide export system periplasmic protein (NCBI ptt file) 88, 133
Cj1451 dut putative dUTPase (NCBI ptt file) 88, 115
Cj1549c Cj1549c putative type I restriction enzyme R protein (NCBI ptt file) 46, 60
Cj1553c Cj1553c putative type I restriction enzyme M protein (NCBI ptt file) 41, 46
Cj1581c Cj1581c putative peptide ABC-transport system ATP-binding protein (NCBI ptt file) 88, 162
Cj1644 ispA geranyltranstransferase (NCBI ptt file) 46, 69
Cj1647 iamA putative ABC transport system ATP-binding protein (NCBI ptt file) 88, 162
Cj1722c Cj1722c hypothetical protein Cj1722c (NCBI ptt file) 88, 118
Cj1723c Cj1723c putative periplasmic protein (NCBI ptt file) 46, 59
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 Cj0508
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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