Organism : Campylobacter jejuni | Module List :
Cjt01 tRNA-Leu

tRNA-Leu (NCBI)

CircVis
Functional Annotations (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cjt01
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cjt01!

Warning: Cjt01 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
7536 2.90e-02 Gt.TaGCtCAG..gg
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7537 2.80e+00 cAGGTCGcGGGTTCAAtTCCC
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7602 1.70e+02 ccAAAagCtct
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7603 3.70e+03 GCCCaGc
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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 Cjt01

Cjt01 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Module neighborhood information for Cjt01

Cjt01 has total of 49 gene neighbors in modules 77, 110
Gene neighbors (49)
Gene Common Name Description Module membership
Cj0055c Cj0055c hypothetical protein Cj0055c (NCBI ptt file) 110, 149
Cj0085c Cj0085c putative amino acid recemase (NCBI ptt file) 77, 157
Cj0106 atpG ATP synthase F1 sector gamma subunit (NCBI ptt file) 60, 110
Cj0205 bacA putative undecaprenol kinase (bacitracin resistance protein) (NCBI ptt file) 98, 110
Cj0282c serB putative phosphoserine phosphatase (NCBI ptt file) 77, 122
Cj0371 Cj0371 putative flagellar motility protein (NCBI ptt file) 13, 110
Cj0377 Cj0377 probable AAA family ATPase (NCBI ptt file) 13, 77
Cj0378c Cj0378c putative integral membrane protein (NCBI ptt file) 77, 168
Cj0433c mraY phospho-N-acetylmuramoyl-pentapeptide- transferase (NCBI ptt file) 77, 125
Cj0529c Cj0529c hypothetical protein Cj0529c (NCBI ptt file) 77, 122
Cj0532 mdh malate dehydrogenase (NCBI ptt file) 11, 110
Cj0558c proA gamma-glutamyl phosphate reductase (NCBI ptt file) 110, 116
Cj0572 ribA GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase (NCBI ptt file) 110, 130
Cj0573 Cj0573 hypothetical protein Cj0573 (NCBI ptt file) 110, 130
Cj0574 ilvI acetolactate synthase large subunit (NCBI ptt file) 11, 110
Cj0575 ilvH acetolactate synthase small subunit (NCBI ptt file) 13, 110
Cj0576 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (NCBI ptt file) 37, 110
Cj0618 Cj0618 hypothetical protein Cj0618 (617 family) (NCBI ptt file) 77, 129
Cj0628 Cj0628 putative lipoprotein (NCBI) 110, 130
Cj0701 Cj0701 putative protease (NCBI ptt file) 110, 141
Cj0802 cysS cysteinyl-tRNA synthetase (NCBI ptt file) 69, 110
Cj0805 Cj0805 putative zinc protease (NCBI ptt file) 110, 122
Cj0821 glmU UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) 104, 110
Cj0899c thiJ 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein (NCBI ptt file) 110, 137
Cj0923c cheR putative MCP protein methyltransferase (NCBI ptt file) 60, 110
Cj0941c Cj0941c putative integral membrane protein (NCBI ptt file) 77, 168
Cj0943 Cj0943 putative periplasmic protein (NCBI ptt file) 17, 77
Cj0954c Cj0954c putative dnaJ-like protein (NCBI ptt file) 26, 77
Cj1060c Cj1060c small hydrophobic protein (NCBI ptt file) 110, 160
Cj1107 Cj1107 hypothetical protein Cj1107 (NCBI ptt file) 77, 114
Cj1178c Cj1178c highly acidic protein (NCBI ptt file) 77, 142
Cj1183c cfa putative cyclopropane-fatty-acyl-phospholipid synthase (NCBI ptt file) 77, 136
Cj1197c gatB Glu-tRNAGln amidotransferase subunit B (NCBI ptt file) 64, 110
Cj1211 Cj1211 putative integral membrane protein (NCBI ptt file) 67, 77
Cj1212c rbn putative ribonuclease BN (NCBI ptt file) 77, 161
Cj1218c ribA putative riboflavin synthase alpha chain (NCBI ptt file) 110, 160
Cj1304 acpP3 putative acyl carrier protein (NCBI ptt file) 77, 89
Cj1310c Cj1310c hypothetical protein Cj1310c (617 family) (NCBI ptt file) 51, 77
Cj1332 ptmA putative oxidoreductase (flagellin modification) (NCBI ptt file) 63, 77
Cj1401c tpiA putative triosephosphate isomerase (NCBI ptt file) 110, 137
Cj1402c pgk phosphoglycerate kinase (NCBI ptt file) 110, 121
Cj1445c kpsE putative capsule polysaccharide export system inner membrane protein (NCBI ptt file) 77, 84
Cj1537c acs acetyl-coenzyme A synthetase (NCBI ptt file) 77, 157
Cj1588c Cj1588c putative transmembrane transport protein (NCBI ptt file) 77, 103
Cj1612 prfA peptide chain release factor 1 (NCBI ptt file) 77, 131
Cj1634c aroC chorismate synthase (NCBI ptt file) 63, 110
Cj1673c recA recA protein (NCBI ptt file) 38, 110
Cjp08 tRNA-Gly tRNA-Gly (NCBI) 77, 85
Cjt01 tRNA-Leu tRNA-Leu (NCBI) 77, 110
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 Cjt01
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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