Organism : Campylobacter jejuni | Module List :
Cj0197c dapB

dihydrodipicolinate reductase (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
Dihydrodipicolinate reductase cog/ cog
cytoplasm go/ cellular_component
dihydrodipicolinate reductase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0197c
(Mouseover regulator name to see its description)

Cj0197c is regulated by 1 influences and regulates 0 modules.
Regulators for Cj0197c dapB (1)
Regulator Module Operator
Cj0757 42 tf

Warning: Cj0197c 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
7466 2.70e+02 GCagcggAagagGg
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7467 4.10e+03 GCTcCAAccG
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7520 7.80e+03 TttCAAGg
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7521 1.00e+04 GGCAATcTTC
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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 Cj0197c

Cj0197c is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Dihydrodipicolinate reductase cog/ cog
cytoplasm go/ cellular_component
dihydrodipicolinate reductase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapB tigr/ tigrfam
Module neighborhood information for Cj0197c

Cj0197c has total of 45 gene neighbors in modules 42, 69
Gene neighbors (45)
Gene Common Name Description Module membership
Cj0025c Cj0025c putative transmembrane symporter (NCBI ptt file) 69, 99
Cj0040 Cj0040 hypothetical protein Cj0040 (NCBI ptt file) 36, 42
Cj0044c Cj0044c hypothetical protein Cj0044c (NCBI ptt file) 42, 145
Cj0069 Cj0069 hypothetical protein Cj0069 (NCBI ptt file) 69, 127
Cj0197c dapB dihydrodipicolinate reductase (NCBI ptt file) 42, 69
Cj0318 fliF flagellar M-ring protein (NCBI ptt file) 25, 42
Cj0401 lysS lysyl-tRNA synthetase (NCBI ptt file) 42, 127
Cj0435 fabG 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 42, 145
Cj0477 rplL 50S ribosomal protein L7 /L12 (NCBI ptt file) 14, 42
Cj0580c Cj0580c putative oxidoreductase (NCBI ptt file) 15, 69
Cj0582 lysC aspartokinase, alpha and beta subunits (NCBI ptt file) 69, 123
Cj0623 hypB hydrogenase isoenzymes formation protein (NCBI ptt file) 10, 42
Cj0624 hypC hydrogenase isoenzymes formation protein (NCBI ptt file) 42, 115
Cj0626 hypE hydrogenase isoenzymes formation protein (NCBI ptt file) 42, 61
Cj0686 gcpE gcpE protein homolog (NCBI ptt file) 42, 100
Cj0715 Cj0715 transthyretin-like periplasmic protein (NCBI ptt file) 42, 112
Cj0771c Cj0771c putative periplasmic protein (NCBI ptt file) 24, 42
Cj0802 cysS cysteinyl-tRNA synthetase (NCBI ptt file) 69, 110
Cj0817 glnH glutamine-binding periplasmic protein (NCBI ptt file) 42, 156
Cj0834c Cj0834c ankyrin repeat-containing possible periplasmic protein (NCBI ptt file) 69, 169
Cj0860 Cj0860 probable integral membrane protein (NCBI ptt file) 65, 69
Cj0894c lytB lytB homolog (NCBI ptt file) 69, 125
Cj0895c aroA 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file) 41, 69
Cj0928 Cj0928 putative integral membrane protein (dedA family) (NCBI ptt file) 8, 69
Cj0933c pycB putative pyruvate carboxylase B subunit (NCBI ptt file) 69, 133
Cj0949c Cj0949c hypothetical protein Cj0949c (NCBI ptt file) 69, 168
Cj0994c argF ornithine carbamoyltransferase (NCBI ptt file) 42, 137
Cj1045c thiG thiG protein (NCBI ptt file) 42, 64
Cj1046c moeB putative molybdopterin biosynthesis protein (NCBI ptt file) 42, 53
Cj1220 groES 10 kD chaperonin (cpn10) (NCBI ptt file) 9, 42
Cj1250 purD phosphoribosylamine--glycine ligase (NCBI ptt file) 42, 61
Cj1260c dnaJ chaperone DnaJ (NCBI ptt file) 42, 55
Cj1277c Cj1277c putative ABC transporter ATP-binding protein (NCBI ptt file) 56, 69
Cj1431c Cj1431c hypothetical protein Cj1431c (NCBI ptt file) 36, 42
Cj1450 Cj1450 putative ATP/GTP-binding protein (NCBI ptt file) 42, 75
Cj1465 Cj1465 hypothetical protein Cj1465 (NCBI ptt file) 42, 86
Cj1510c fdhB putative formate dehydrogenase iron-sulfur subunit (NCBI ptt file) 42, 156
Cj1513c Cj1513c possible periplasmic protein (NCBI ptt file) 42, 95
Cj1514c Cj1514c hypothetical protein Cj1514c (NCBI ptt file) 42, 115
Cj1570c nuoJ NADH dehydrogenase I chain J (NCBI ptt file) 42, 54
Cj1573c nuoG probable NADH dehydrogenase I chain G (NCBI ptt file) 69, 166
Cj1574c Cj1574c hypothetical protein Cj1574c (NCBI ptt file) 24, 42
Cj1639 Cj1639 nifU protein homolog (NCBI ptt file) 69, 137
Cj1644 ispA geranyltranstransferase (NCBI ptt file) 46, 69
Cjt02 tRNAAsp tRNA-Asp (RefSeq) 42, 132
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 Cj0197c
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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