Organism : Campylobacter jejuni | Module List :
Cj0891c serA

D-3-phosphoglycerate dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PGDH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0891c
(Mouseover regulator name to see its description)

Cj0891c is regulated by 3 influences and regulates 0 modules.
Regulators for Cj0891c serA (3)
Regulator Module Operator
Cj1000 63 tf
Cj1001 63 tf
Cj1349c 63 tf

Warning: Cj0891c 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
7508 1.20e+03 GGCACaCc
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7509 5.10e+03 CaCCgCc
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7678 2.60e+00 CAAGGA.AA
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7679 2.50e+03 CGATGTTAATCAATGCTTAATCC
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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 Cj0891c

Cj0891c is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PGDH tigr/ tigrfam
Module neighborhood information for Cj0891c

Cj0891c has total of 41 gene neighbors in modules 63, 148
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0035c Cj0035c putative efflux protein (NCBI ptt file) 24, 148
Cj0054c Cj0054c hypothetical protein Cj0054c (NCBI ptt file) 51, 148
Cj0164c ubiA putative 4-hydroxybenzoate octaprenyltransferase (NCBI ptt file) 63, 149
Cj0174c Cj0174c putative iron-uptake ABC transport system permease protein (NCBI ptt file) 7, 148
Cj0202c Cj0202c hypothetical protein Cj0202c (NCBI ptt file) 63, 155
Cj0271 Cj0271 bacterioferritin comigratory protein homolog (NCBI ptt file) 52, 63
Cj0276 mreB homolog of E. coli rod shape-determining protein (NCBI ptt file) 76, 148
Cj0303c modA putative molybdate-binding lipoprotein (NCBI ptt file) 123, 148
Cj0387 aroK shikimate kinase (NCBI ptt file) 6, 63
Cj0388 trpS tryptophanyl-tRNA synthetase (NCBI ptt file) 63, 166
Cj0444 Cj0444 None 63, 107
Cj0515 Cj0515 putative periplasmic protein (NCBI ptt file) 99, 148
Cj0544 Cj0544 putative integral memnbrane protein (NCBI ptt file) 148, 161
Cj0561c Cj0561c possible periplasmic protein (NCBI ptt file) 58, 148
Cj0646 Cj0646 putative lipoprotein (NCBI ptt file) 19, 63
Cj0718 dnaE DNA polymerase III, alpha chain (NCBI ptt file) 112, 148
Cj0730 Cj0730 putative ABC transport system permease (NCBI ptt file) 63, 164
Cj0854c Cj0854c putative periplasmic protein (NCBI ptt file) 63, 120
Cj0891c serA D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 63, 148
Cj1000 Cj1000 putative transcriptional regulator (lysR family) (NCBI ptt file) 44, 63
Cj1030c lepA lepA GTP-binding protein homolog (NCBI ptt file) 63, 160
Cj1080c Cj1080c hypothetical protein Cj1080c (NCBI ptt file) 118, 148
Cj1086c Cj1086c hypothetical protein Cj1086c (NCBI ptt file) 63, 81
Cj1146c waaV putative glucosyltransferase (NCBI ptt file) 63, 149
Cj1217c Cj1217c hypothetical protein Cj1217c (NCBI ptt file) 26, 148
Cj1316c Cj1316c hypothetical protein Cj1316c (NCBI ptt file) 63, 144
Cj1327 neuB2 N-acetylneuraminic acid synthetase (NCBI ptt file) 63, 117
Cj1331 ptmB acylneuraminate cytidylyltransferase (flagellin modification) (NCBI ptt file) 63, 146
Cj1332 ptmA putative oxidoreductase (flagellin modification) (NCBI ptt file) 63, 77
Cj1333 Cj1333 hypothetical protein Cj1333 (1318 family) (NCBI ptt file) 63, 109
Cj1374c Cj1374c hypothetical protein Cj1374c (NCBI ptt file) 148, 158
Cj1375 Cj1375 putative efflux protein (NCBI ptt file) 128, 148
Cj1413c Cj1413c possible polysaccharide modification protein (NCBI ptt file) 117, 148
Cj1424c gmhA2 putative phosphoheptose isomerase (NCBI ptt file) 109, 148
Cj1427c Cj1427c putative sugar-nucleotide epimerase/dehydratease (NCBI ptt file) 109, 148
Cj1428c fcl putative fucose synthetase (NCBI ptt file) 109, 148
Cj1458c thiL putative thiamin-monophosphate kinase (NCBI ptt file) 44, 63
Cj1562 Cj1562 hypothetical protein Cj1562 (NCBI ptt file) 19, 63
Cj1634c aroC chorismate synthase (NCBI ptt file) 63, 110
Cj1717c leuC 3-isopropylmalate dehydratase large subunit (NCBI ptt file) 45, 148
Cj1727c metY putative O-acetylhomoserine (thiol)-lyase (NCBI ptt file) 63, 83
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 Cj0891c
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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