Organism : Campylobacter jejuni | Module List :
Cj0166 miaA

tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0166
(Mouseover regulator name to see its description)

Cj0166 is regulated by 8 influences and regulates 0 modules.
Regulators for Cj0166 miaA (8)
Regulator Module Operator
Cj0123c 17 tf
Cj0466 17 tf
Cj0480c 17 tf
Cj0670 17 tf
Cj1273c 17 tf
Cj0480c 152 tf
Cj0571 152 tf
Cj0670 152 tf

Warning: Cj0166 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
7416 9.90e+01 AgCctaAg.ca
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7417 3.40e+03 CTGTCTTCATAGTATAAAACCG
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7686 7.00e+02 ctT.TGC..cC
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7687 4.50e+03 cccACAGGTTG
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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 Cj0166

Cj0166 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
tRNA delta(2)-isopentenylpyrophosphate transferase cog/ cog
dimethylallyltranstransferase activity go/ molecular_function
ATP binding go/ molecular_function
tRNA processing go/ biological_process
biosynthetic process go/ biological_process
tRNA dimethylallyltransferase activity go/ molecular_function
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
miaA tigr/ tigrfam
Module neighborhood information for Cj0166

Cj0166 has total of 52 gene neighbors in modules 17, 152
Gene neighbors (52)
Gene Common Name Description Module membership
Cj0038c Cj0038c putative membrane protein (NCBI ptt file) 105, 152
Cj0123c Cj0123c putative transcriptional regulator (NCBI ptt file) 17, 29
Cj0125c Cj0125c dksA-like protein (NCBI ptt file) 17, 23
Cj0126c Cj0126c hypothetical protein Cj0126c (NCBI ptt file) 17, 68
Cj0139 Cj0139 putative endonuclease (NCBI ptt file) 49, 152
Cj0166 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) 17, 152
Cj0190c Cj0190c hypothetical protein Cj0190c (NCBI ptt file) 105, 152
Cj0293 surE SurE protein homolog (NCBI ptt file) 17, 129
Cj0363c Cj0363c putative oxidoreductase (NCBI ptt file) 17, 57
Cj0376 Cj0376 putative periplasmic protein (NCBI ptt file) 13, 17
Cj0422c Cj0422c putative H-T-H containing protein (NCBI ptt file) 15, 152
Cj0466 Cj0466 putative transcriptional regulator (NCBI ptt file) 9, 17
Cj0563 Cj0563 hypothetical protein Cj0563 (NCBI ptt file) 15, 152
Cj0567 Cj0567 hypothetical protein Cj0567 (NCBI ptt file) 50, 152
Cj0584 Cj0584 hypothetical protein Cj0584 (NCBI ptt file) 15, 152
Cj0650 Cj0650 putative ATP /GTP binding protein (NCBI ptt file) 7, 17
Cj0679 kdpD' truncated KdpD protein (NCBI ptt file) 17, 54
Cj0685c Cj0685c possible sugar transferase (NCBI ptt file) 72, 152
Cj0728 Cj0728 putative periplasmic protein (NCBI ptt file) 15, 152
Cj0729 Cj0729 hypothetical protein Cj0729 (NCBI ptt file) 101, 152
Cj0731 Cj0731 putative ABC transport system permease (NCBI ptt file) 1, 152
Cj0732 Cj0732 ABC transport system ATP-binding protein (NCBI ptt file) 37, 152
Cj0741 Cj0741 hypothetical protein Cj0741 (NCBI ptt file) 116, 152
Cj0748 Cj0748 hypothetical protein Cj0748 (NCBI ptt file) 71, 152
Cj0815 Cj0815 hypothetical protein Cj0815 (NCBI ptt file) 152, 167
Cj0856 lepP signal peptidase I (NCBI ptt file) 17, 43
Cj0861c pabA para-aminobenzoate synthase glutamine amidotransferase component II (NCBI ptt file) 38, 152
Cj0862c pabB para-aminobenzoate synthase component I (NCBI ptt file) 17, 89
Cj0943 Cj0943 putative periplasmic protein (NCBI ptt file) 17, 77
Cj1078 Cj1078 putative periplasmic protein (NCBI ptt file) 17, 72
Cj1108 clpA ATP-dependent CLP protease ATP-binding subunit (NCBI ptt file) 17, 153
Cj1116c ftsH membrane bound zinc metallopeptidase (NCBI ptt file) 17, 131
Cj1160c Cj1160c small hydrophobic protein (NCBI ptt file) 58, 152
Cj1226c Cj1226c putative two-component sensor (NCBI ptt file) 17, 64
Cj1229 cbpA putative curved-DNA binding protein (NCBI ptt file) 17, 64
Cj1231 kefB putative glutathione-regulated potassium-efflux system protein (NCBI ptt file) 17, 64
Cj1233 Cj1233 putative hydrolase (NCBI ptt file) 17, 64
Cj1247c Cj1247c hypothetical protein Cj1247c (NCBI ptt file) 7, 17
Cj1296 Cj1296 hypothetical protein Cj1296 (NCBI ptt file) 152, 165
Cj1313 Cj1313 possible flagellar protein (NCBI ptt file) 123, 152
Cj1334 Cj1334 hypothetical prootein Cj1334 (1318 family) (NCBI ptt file) 17, 121
Cj1378 selA L-seryl-tRNA(SeC) selenium transferase (NCBI ptt file) 17, 159
Cj1404 Cj1404 hypothetical protein Cj1404 (NCBI ptt file) 53, 152
Cj1426c Cj1426c hypothetical protein Cj1426c (NCBI ptt file) 17, 36
Cj1457c Cj1457c ypothetical protein Cj1457c (NCBI ptt file) 144, 152
Cj1522c Cj1522c hypothetical protein Cj1522c (NCBI ptt file) 152, 155
Cj1621 Cj1621 putative periplasmic protein (NCBI ptt file) 25, 152
Cj1676 murB putative UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 96, 152
Cj1679 Cj1679 hypothetical protein Cj1679 (NCBI ptt file) 15, 152
Cj1684c Cj1684c putative transmembrane transport protein (NCBI ptt file) 17, 117
Cj1716c leuD putative 3-isopropylmalate dehydratase small subunit (NCBI ptt file) 17, 70
Cjp11 Cjp11 None 5, 152
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 Cj0166
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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