Organism : Campylobacter jejuni | Module List :
Cj0405 aroE

shikimate 5-dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Shikimate 5-dehydrogenase cog/ cog
shikimate 3-dehydrogenase (NADP+) activity go/ molecular_function
cytoplasm go/ cellular_component
NADP binding go/ molecular_function
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
aroE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0405
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0405!

Warning: Cj0405 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
7502 3.30e+04 GCaATGcCC
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7503 3.80e+04 GAAAGGAC
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7712 1.60e+03 GgAAcaaTTATTGCT
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7713 1.50e+04 CCaAAACCTcAaCaATAAcaTTcC
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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 Cj0405

Cj0405 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Shikimate 5-dehydrogenase cog/ cog
shikimate 3-dehydrogenase (NADP+) activity go/ molecular_function
cytoplasm go/ cellular_component
NADP binding go/ molecular_function
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
aroE tigr/ tigrfam
Module neighborhood information for Cj0405

Cj0405 has total of 44 gene neighbors in modules 60, 165
Gene neighbors (44)
Gene Common Name Description Module membership
Cj0080 Cj0080 putative membrane protein (NCBI ptt file) 44, 60
Cj0106 atpG ATP synthase F1 sector gamma subunit (NCBI ptt file) 60, 110
Cj0149c hom homoserine dehydrogenase (NCBI ptt file) 62, 165
Cj0223 Cj0223 None 60, 71
Cj0361 lspA lipoprotein signal peptidase (NCBI ptt file) 52, 165
Cj0362 Cj0362 putative integral membrane protein (NCBI ptt file) 33, 165
Cj0385c Cj0385c putative integral membrane protein (NCBI ptt file) 60, 82
Cj0405 aroE shikimate 5-dehydrogenase (NCBI ptt file) 60, 165
Cj0592c Cj0592c putative periplasmic protein (NCBI ptt file) 45, 60
Cj0615 pstA putative phosphate transport system permease protein (NCBI ptt file) 132, 165
Cj0619 Cj0619 putative integral membrane protein (NCBI ptt file) 60, 144
Cj0644 Cj0644 hypothetical protein Cj0644 (NCBI ptt file) 44, 165
Cj0683 Cj0683 putative periplasmic protein (NCBI ptt file) 88, 165
Cj0725c mog molybdopterin biosynthesis protein (NCBI ptt file) 143, 165
Cj0767c kdtB 3-deoxy-D-manno-octulosonic-acid transferase (NCBI ptt file) 36, 60
Cj0923c cheR putative MCP protein methyltransferase (NCBI ptt file) 60, 110
Cj0962 Cj0962 putative acetyltransferase (NCBI ptt file) 47, 60
Cj0963 Cj0963 hypothetical protein Cj0963 (NCBI ptt file) 37, 60
Cj0987c Cj0987c putative integral membrane protein (NCBI ptt file) 32, 165
Cj0988c Cj0988c very hypothetical protein Cj0988c (NCBI ptt file) 155, 165
Cj1073c lon ATP-dependent protease La (NCBI ptt file) 129, 165
Cj1097 Cj1097 putative transmembrane transport protein (NCBI ptt file) 37, 60
Cj1114c pssA CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 60, 150
Cj1117c prmA possible ribosomal protein methyltransferase (NCBI ptt file) 60, 160
Cj1132c Cj1132c hypothetical protein Cj1132c (NCBI ptt file) 33, 165
Cj1205c radA putative DNA repair protein RadA (ATP-dependant protease) (NCBI ptt file) 36, 60
Cj1207c Cj1207c putative lipoprotein thiredoxin (NCBI ptt file) 51, 165
Cj1214c Cj1214c hypothetical protein Cj1214c (NCBI ptt file) 94, 165
Cj1294 Cj1294 putative aminotransferase (degT family) (NCBI ptt file) 120, 165
Cj1295 Cj1295 hypothetical protein Cj1295 (NCBI ptt file) 120, 165
Cj1296 Cj1296 hypothetical protein Cj1296 (NCBI ptt file) 152, 165
Cj1297 Cj1297 hypotehtical protein Cj1297 (NCBI ptt file) 120, 165
Cj1299 acpP2 putative acyl carrier protein (NCBI ptt file) 120, 165
Cj1300 Cj1300 hypothetical protein Cj1300 (NCBI ptt file) 133, 165
Cj1325 Cj1325 putative methyltransferase (NCBI) 117, 165
Cj1409 acpS putative holo-[acyl-carrier protein] synthase (NCBI ptt file) 136, 165
Cj1432c Cj1432c putative sugar transferase (NCBI ptt file) 60, 109
Cj1435c Cj1435c hypothetical protein Cj1435c (NCBI ptt file) 60, 150
Cj1442c Cj1442c hypothetical protein Cj1442c (NCBI ptt file) 6, 60
Cj1492c Cj1492c putative two-component sensor (NCBI ptt file) 38, 60
Cj1503c putA putative proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI ptt file) 158, 165
Cj1549c Cj1549c putative type I restriction enzyme R protein (NCBI ptt file) 46, 60
Cj1637c Cj1637c putative periplasmic protein (NCBI ptt file) 75, 165
Cj1719c leuA 2-isopropylmalate synthase (NCBI ptt file) 24, 165
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 Cj0405
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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