Organism : Campylobacter jejuni | Module List :
Cj1085c mfd

transcription-repair coupling factor (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
Nucleotide excision repair kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1085c
(Mouseover regulator name to see its description)

Cj1085c is regulated by 3 influences and regulates 0 modules.
Regulators for Cj1085c mfd (3)
Regulator Module Operator
Cj0473 151 tf
Cj0479 151 tf
Cj0670 151 tf

Warning: Cj1085c 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
7558 1.10e+04 CTcaATGGGtGG
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7559 1.80e+04 GAGCcTG
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7684 1.10e+02 ctaa.ccTtTGgctat.gCTTttc
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7685 4.30e+03 GGcACAC
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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 Cj1085c

Cj1085c is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
Nucleotide excision repair kegg/ kegg pathway
Module neighborhood information for Cj1085c

Cj1085c has total of 53 gene neighbors in modules 88, 151
Gene neighbors (53)
Gene Common Name Description Module membership
Cj0081 cydA cytochrome bd oxidase subunit I (NCBI ptt file) 44, 151
Cj0107 atpD ATP synthase F1 sector beta subunit (NCBI ptt file) 111, 151
Cj0108 atpC ATP synthase F1 sector epsilon subunit (NCBI ptt file) 111, 151
Cj0109 exbB3 exbB olQ family transport protein (VIMSS-AUTO) 150, 151
Cj0110 exbD3 exbD 150, 151
Cj0111 Cj0111 periplasmic protein (NCBI ptt file) 150, 151
Cj0112 Cj0112 periplasmic protein (NCBI ptt file) 150, 151
Cj0116 fabD malonyl CoA-acyl carrier protein transacylase (NCBI ptt file) 150, 151
Cj0117 pfs 5'-methylthioadenosineS-adenosylhomocysteine nucleosidase (VIMSS-AUTO) 111, 151
Cj0118 Cj0118 hypothetical protein Cj0118 (NCBI ptt file) 150, 151
Cj0119 Cj0119 hypothetical protein Cj0119 (NCBI ptt file) 150, 151
Cj0120 Cj0120 hypothetical protein Cj0120 (NCBI ptt file) 88, 150
Cj0121 Cj0121 hypothetical protein Cj0121 (NCBI ptt file) 150, 151
Cj0154c Cj0154c putative methylase (NCBI ptt file) 14, 151
Cj0206 thrS threonyl-tRNA synthetase (NCBI ptt file) 65, 151
Cj0244 rpmI 50s ribosomal protein L35 (NCBI ptt file) 138, 151
Cj0245 rplT 50S ribosomal protein L20 (NCBI ptt file) 111, 151
Cj0246c Cj0246c putative MCP-domain signal transduction protein (NCBI ptt file) 47, 88
Cj0248 Cj0248 hypothetical protein Cj0248 (NCBI ptt file) 47, 88
Cj0275 clpX ATP-dependent clp protease ATP-binding subunit clpX (NCBI ptt file) 14, 151
Cj0315 Cj0315 hypothetical protein Cj0315 (NCBI ptt file) 52, 151
Cj0328c fabH 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) 104, 151
Cj0329c plsX putative fatty acidphospholipid synthesis protein (VIMSS-AUTO) 117, 151
Cj0330c rpmF 50S ribosomal protein L32 (NCBI ptt file) 14, 151
Cj0347 trpF N-(5'-phosphoribosyl)anthranilate isomerase (NCBI ptt file) 88, 104
Cj0461c Cj0461c putative integral membrane protein (NCBI ptt file) 46, 88
Cj0505c Cj0505c putative aminotransferase (degT family) (NCBI ptt file) 47, 88
Cj0508 pbpA penicillin-binding protein (NCBI ptt file) 46, 88
Cj0585 folP putative dihydropteroate synthase (NCBI ptt file) 88, 117
Cj0605 Cj0605 putative amidohydrolase (NCBI ptt file) 88, 161
Cj0608 Cj0608 putative outer membrane protein (NCBI ptt file) 88, 138
Cj0647 Cj0647 hypothetical protein Cj0647 (NCBI ptt file) 141, 151
Cj0683 Cj0683 putative periplasmic protein (NCBI ptt file) 88, 165
Cj0775c valS valyl-tRNA synthetase (NCBI ptt file) 59, 88
Cj0880c Cj0880c hypothetical protein Cj0880c (NCBI ptt file) 79, 88
Cj0902 glnQ putative glutamine transport ATP-binding protein (NCBI ptt file) 48, 88
Cj1013c Cj1013c putative membrane protein (NCBI ptt file) 128, 151
Cj1014c livF branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) 128, 151
Cj1015c livG branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) 104, 151
Cj1017c livH branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) 128, 151
Cj1085c mfd transcription-repair coupling factor (NCBI ptt file) 88, 151
Cj1311 neuA2 acylneuraminate cytidylyltransferase (NCBI ptt file) 18, 88
Cj1367c Cj1367c possible nucleotidyltransferase (NCBI ptt file) 88, 125
Cj1372 Cj1372 putative periplasmic protein (NCBI ptt file) 41, 88
Cj1436c Cj1436c putative aminotransferase (NCBI ptt file) 88, 125
Cj1444c kpsD putative capsule polysaccharide export system periplasmic protein (NCBI ptt file) 88, 133
Cj1451 dut putative dUTPase (NCBI ptt file) 88, 115
Cj1581c Cj1581c putative peptide ABC-transport system ATP-binding protein (NCBI ptt file) 88, 162
Cj1647 iamA putative ABC transport system ATP-binding protein (NCBI ptt file) 88, 162
Cj1688c secY preprotein translocase subunit (NCBI ptt file) 128, 151
Cj1710c Cj1710c hypothetical protein Cj1710c (NCBI ptt file) 128, 151
Cj1711c ksgA putative dimethyladenosine transferase (16S rRNA dimethylase) (NCBI ptt file) 128, 151
Cj1722c Cj1722c hypothetical protein Cj1722c (NCBI ptt file) 88, 118
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 Cj1085c
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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