Organism : Campylobacter jejuni | Module List :
Cj1167 ldh

putative L-lactate dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
Malate/lactate dehydrogenases cog/ cog
L-lactate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
glycolysis go/ biological_process
tricarboxylic acid cycle intermediate metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1167
(Mouseover regulator name to see its description)

Cj1167 is regulated by 8 influences and regulates 0 modules.
Regulators for Cj1167 ldh (8)
Regulator Module Operator
Cj0368c 45 tf
Cj0571 45 tf
Cj0670 45 tf
Cj1595 45 tf
Cj0400 101 tf
Cj0571 101 tf
Cj1042c 101 tf
Cj1561 101 tf

Warning: Cj1167 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
7472 2.90e+03 cCtcAAagcct
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7473 7.30e+03 CttGcTgcTG
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7584 3.50e+02 gc.aGaag.tGcaa.
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7585 9.10e+03 AaAAgTtCGCc
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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 Cj1167

Cj1167 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Malate/lactate dehydrogenases cog/ cog
L-lactate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
glycolysis go/ biological_process
tricarboxylic acid cycle intermediate metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for Cj1167

Cj1167 has total of 51 gene neighbors in modules 45, 101
Gene neighbors (51)
Gene Common Name Description Module membership
Cj0070c Cj0070c very hypothetical protein Cj0070c (NCBI ptt file) 29, 45
Cj0140 Cj0140 hypothetical protein Cj0140 (NCBI ptt file) 40, 101
Cj0142c Cj0142c ABC transporter ATP-binding protein (NCBI ptt file) 45, 55
Cj0180 exbD1 biopolymer transport protein (NCBI ptt file) 101, 167
Cj0184c Cj0184c possible serine 23, 101
Cj0230c Cj0230c hypothetical protein Cj0230c (NCBI ptt file) 23, 101
Cj0300c modC putative molybdenum transport ATP-binding protein (NCBI ptt file) 101, 105
Cj0348 trpB tryptophan synthase beta chain (NCBI ptt file) 45, 145
Cj0411 Cj0411 putative ATP /GTP binding protein (NCBI ptt file) 45, 124
Cj0523 Cj0523 putative membrane protein (NCBI ptt file) 23, 101
Cj0592c Cj0592c putative periplasmic protein (NCBI ptt file) 45, 60
Cj0599 Cj0599 putative periplasmic protein (NCBI ptt file) 45, 144
Cj0602c Cj0602c hypothetical protein Cj0602c (NCBI ptt file) 50, 101
Cj0627 hypA hydrogenase expression /formation protein (NCBI ptt file) 45, 145
Cj0649 Cj0649 hypothetical protein Cj0649 (NCBI ptt file) 45, 105
Cj0659c Cj0659c putative periplasmic protein (NCBI ptt file) 101, 124
Cj0692c Cj0692c putative membrane protein (NCBI ptt file) 45, 55
Cj0722c Cj0722c putative DNA methylase (NCBI ptt file) 101, 144
Cj0729 Cj0729 hypothetical protein Cj0729 (NCBI ptt file) 101, 152
Cj0763c cysE serine acetyltransferase (NCBI ptt file) 44, 45
Cj0769c Cj0769c putative periplasmic protein (NCBI ptt file) 45, 116
Cj0803 msbA lipid export ABC transport protein (NCBI ptt file) 45, 55
Cj0814 Cj0814 hypothetical protein Cj0814 (NCBI ptt file) 45, 167
Cj0831c trmA tRNA (uracil-5-)-methyltransferase (NCBI ptt file) 45, 51
Cj0836 ogt methylated-DNA--protein-cysteine methyltransferase (NCBI ptt file) 45, 145
Cj0926 Cj0926 putative membrane protein (NCBI ptt file) 12, 101
Cj0948c Cj0948c putative transmembrane transport protein (NCBI ptt file) 45, 96
Cj0967 Cj0967 putative periplasmic protein (NCBI ptt file) 99, 101
Cj1095 Cj1095 putative integral membrane protein (NCBI ptt file) 7, 101
Cj1113 Cj1113 hypothetical protein Cj1113 (NCBI ptt file) 101, 167
Cj1133 waaC putative lipopolysaccharide heptosyltransferase (NCBI ptt file) 100, 101
Cj1134 htrB putative lipid A biosynthesis lauroyl acyltransferase (NCBI ptt file) 45, 46
Cj1135 Cj1135 putative two-domain glycosyltransferase (NCBI ptt file) 45, 144
Cj1136 Cj1136 putative galactosyltransferase (NCBI ptt file) 15, 101
Cj1142 neuC1 putative N-acetylglucosamine-6-phosphate 2-epimerase/N-acetylglucosamine-6-phosphatase (NCBI ptt file) 45, 67
Cj1143 neuA1 acylneuraminate cytidylyltransferase (NCBI ptt file) 40, 101
Cj1162c Cj1162c hypothetical protein Cj1162c (NCBI ptt file) 7, 101
Cj1167 ldh putative L-lactate dehydrogenase (NCBI ptt file) 45, 101
Cj1252 Cj1252 putative periplasmic protein (NCBI ptt file) 101, 122
Cj1321 Cj1321 putative transferase (NCBI ptt file) 101, 105
Cj1322 Cj1322 hypothetical protein Cj1322 (NCBI ptt file) 7, 101
Cj1328 neuC2 putative N-acetylglucosamine-6-phosphate 2-epimerase/N-acetylglucosamine-6-phosphatase (NCBI ptt file) 101, 108
Cj1329 Cj1329 putative sugar-phosphate nucleotide transferase (NCBI ptt file) 101, 117
Cj1406c Cj1406c putative periplasmic protein (NCBI ptt file) 45, 145
Cj1414c Cj1414c possible polysaccharide modification protein (NCBI ptt file) 7, 101
Cj1475c Cj1475c hypothetical protein Cj1475c (NCBI ptt file) 39, 45
Cj1560 Cj1560 45, 81
Cj1587c Cj1587c putative ABC transporter (NCBI ptt file) 7, 101
Cj1648 Cj1648 possible ABC transport system periplasmic substrate-binding protein (NCBI ptt file) 101, 108
Cj1649 Cj1649 putative lipoprotein (NCBI ptt file) 101, 105
Cj1717c leuC 3-isopropylmalate dehydratase large subunit (NCBI ptt file) 45, 148
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 Cj1167
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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