Organism : Campylobacter jejuni | Module List :
Cj0956c thdF

putative thiophene and furan oxidation protein (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
Predicted GTPase cog/ cog
GTPase activity go/ molecular_function
phosphoglycerate dehydrogenase activity go/ molecular_function
GTP binding go/ molecular_function
intracellular go/ cellular_component
tRNA modification go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
small_GTP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0956c
(Mouseover regulator name to see its description)

Cj0956c is regulated by 3 influences and regulates 0 modules.
Regulators for Cj0956c thdF (3)
Regulator Module Operator
Cj0571 96 tf
Cj1533c 96 tf
Cj1552c 96 tf

Warning: Cj0956c 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
7544 2.10e+03 CCCTTTcGGG
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7545 2.10e+03 gTtaTGAaGAtGtaGaAttTgc
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7574 1.60e+03 GGcAGCGaC
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7575 4.50e+03 GTctgcaagattGcc
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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 Cj0956c

Cj0956c is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Predicted GTPase cog/ cog
GTPase activity go/ molecular_function
phosphoglycerate dehydrogenase activity go/ molecular_function
GTP binding go/ molecular_function
intracellular go/ cellular_component
tRNA modification go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
small_GTP tigr/ tigrfam
Module neighborhood information for Cj0956c

Cj0956c has total of 50 gene neighbors in modules 81, 96
Gene neighbors (50)
Gene Common Name Description Module membership
Cj0005c Cj0005c putative molybdenum containing oxidoreductase (NCBI ptt file) 39, 81
Cj0096 Cj0096 putative GTP-binding protein (NCBI ptt file) 18, 96
Cj0151c Cj0151c putative periplasmic protein (NCBI ptt file) 33, 81
Cj0162c Cj0162c putative periplasmic protein (NCBI ptt file) 56, 81
Cj0167c Cj0167c putative integral membrane protein (NCBI ptt file) 96, 104
Cj0226 argB acetylglutamate kinase (NCBI ptt file) 96, 104
Cj0227 argD acetylornithine aminotransferase (NCBI ptt file) 96, 104
Cj0252 moaC molybdenum cofactor biosynthesis protein C (NCBI ptt file) 19, 81
Cj0306c bioF 8-amino-7-oxononanoate synthase (NCBI ptt file) 96, 104
Cj0373 Cj0373 putative D-2-hydroxyacid dehydrogenase (NCBI ptt file) 13, 81
Cj0381c pyrF orotidine 5'-phosphate decarboxylase (NCBI ptt file) 81, 98
Cj0406c Cj0406c putative lipoprotein (NCBI ptt file) 81, 161
Cj0454c Cj0454c putative membrane protein (NCBI ptt file) 37, 81
Cj0467 Cj0467 amino-acid ABC transporter integral membrane protein (NCBI ptt file) 56, 81
Cj0503c hemH putative ferrochelatase (NCBI ptt file) 23, 96
Cj0579c Cj0579c hypothetical protein Cj0579c (NCBI ptt file) 81, 116
Cj0583 Cj0583 hypothetical protein Cj0583 (NCBI ptt file) 81, 162
Cj0610c Cj0610c putative periplasmic protein (NCBI ptt file) 39, 81
Cj0645 Cj0645 putative secreted transglycosylase (NCBI ptt file) 81, 145
Cj0652 pbpC penicillin-binding protein (NCBI ptt file) 96, 109
Cj0678 Cj0678 None 96, 100
Cj0747 Cj0747 hypothetical protein Cj0747 (NCBI ptt file) 23, 96
Cj0810 nadE putative NH(3)-dependent NAD(+) synthetase (NCBI ptt file) 81, 130
Cj0812 thrC threonine synthase (NCBI ptt file) 11, 81
Cj0934c Cj0934c putative transmembrane transport protein (NCBI ptt file) 81, 154
Cj0948c Cj0948c putative transmembrane transport protein (NCBI ptt file) 45, 96
Cj0956c thdF putative thiophene and furan oxidation protein (NCBI ptt file) 81, 96
Cj1002c Cj1002c hypothetical protein Cj1002c (NCBI ptt file) 37, 81
Cj1028c Cj1028c possible purine/pyrimidine phosphoribosyltransferase (NCBI ptt file) 81, 104
Cj1086c Cj1086c hypothetical protein Cj1086c (NCBI ptt file) 63, 81
Cj1101 Cj1101 ATP-dependent DNA helicase (NCBI ptt file) 7, 96
Cj1104 Cj1104 hypothetical proteinCj1104 (NCBI ptt file) 79, 81
Cj1109 aat putative leucyl/phenylalanyl-tRNA--protein transferase (NCBI ptt file) 96, 109
Cj1123c wlaI putative transferase (NCBI ptt file) 96, 109
Cj1245c Cj1245c putative membrane protein (NCBI ptt file) 23, 96
Cj1258 Cj1258 possible phosphotyrosine protein phosphatase (NCBI ptt file) 38, 81
Cj1312 Cj1312 possible flagellar protein (NCBI ptt file) 38, 81
Cj1323 Cj1323 hypothetical protein Cj1323 (NCBI ptt file) 18, 81
Cj1360c Cj1360c putative proteolysis tag for 10Sa_RNA (NCBI ptt file) 86, 96
Cj1379 selB putative selenocysteine-specific elongation factor (NCBI ptt file) 44, 81
Cj1439c glf UDP-galactopyranose mutase (NCBI ptt file) 81, 98
Cj1453c Cj1453c hypothetical protein Cj1453c (NCBI ptt file) 48, 96
Cj1473c Cj1473c putative ATP/GTP-binding protein (NCBI ptt file) 23, 96
Cj1532 Cj1532 possible periplasmic protein (NCBI ptt file) 81, 158
Cj1552c Cj1552c hypothetical protein Cj1552c (NCBI ptt file) 76, 96
Cj1560 Cj1560 45, 81
Cj1620c mutY A/G-specific adenine glycosylase (NCBI ptt file) 96, 109
Cj1676 murB putative UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) 96, 152
Cj1677 Cj1677 putative lipoprotein (NCBI) 81, 150
VIMSS47534 VIMSS47534 None 96, 108
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 Cj0956c
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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