Organism : Campylobacter jejuni | Module List :
Cj0480c

putative transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0480c
(Mouseover regulator name to see its description)

Cj0480c is regulated by 2 influences and regulates 20 modules.
Regulators for Cj0480c (2)
Regulator Module Operator
Cj0480c 50 tf
Cj0670 50 tf

Warning: Cj0480c 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
7482 1.30e+03 .gcta.tttcaAa.cCt.tgC
Loader icon
7483 2.70e+03 GCGG.aTT
Loader icon
7626 8.10e+02 cAcCCC
Loader icon
7627 3.10e+03 TAAgCactAacagac
Loader icon
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 Cj0480c

Cj0480c is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for Cj0480c

Cj0480c has total of 40 gene neighbors in modules 50, 122
Gene neighbors (40)
Gene Common Name Description Module membership
Cj0009 gltD glutamate synthase (NADPH) small subunit (NCBI ptt file) 50, 155
Cj0010c rnhB ribonuclease HII (NCBI ptt file) 22, 50
Cj0026c Cj0026c hypothetical protein Cj0026c (NCBI ptt file) 50, 68
Cj0281c tal putative transaldolase (NCBI ptt file) 117, 122
Cj0282c serB putative phosphoserine phosphatase (NCBI ptt file) 77, 122
Cj0325 xseA exodeoxyribonuclease VII large subunit (NCBI ptt file) 41, 122
Cj0418c Cj0418c hypothetical protein Cj0418c (NCBI ptt file) 32, 50
Cj0480c Cj0480c putative transcriptional regulator (NCBI ptt file) 50, 122
Cj0497 Cj0497 putative lipoprotein (NCBI ptt file) 50, 100
Cj0529c Cj0529c hypothetical protein Cj0529c (NCBI ptt file) 77, 122
Cj0541 Cj0541 polyprenyl synthetase (NCBI ptt file) 46, 50
Cj0542 hemA glutamyl-tRNA reductase (NCBI ptt file) 8, 122
Cj0567 Cj0567 hypothetical protein Cj0567 (NCBI ptt file) 50, 152
Cj0568 Cj0568 hypothetical protein Cj0568 (NCBI ptt file) 49, 50
Cj0591c Cj0591c putative lipoprotein (NCBI ptt file) 50, 167
Cj0602c Cj0602c hypothetical protein Cj0602c (NCBI ptt file) 50, 101
Cj0680c uvrB excinuclease ABC subunit B (NCBI ptt file) 50, 53
Cj0795c murF putative UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-- ligase (NCBI ptt file) 122, 164
Cj0805 Cj0805 putative zinc protease (NCBI ptt file) 110, 122
Cj0905c alr alanine racemase (NCBI ptt file) 122, 125
Cj0916c Cj0916c hypothetical protein Cj0916c (NCBI ptt file) 38, 50
Cj0938c aas putative 2-acylglycerophosphoethanolamine acyltransferase / acyl-acyl carrier protein synthetase (NCBI ptt file) 48, 122
Cj0944c Cj0944c putative periplasmic protein (NCBI ptt file) 57, 122
Cj0951c Cj0951c putative MCP-domain signal transduction protein (NCBI ptt file) 47, 122
Cj0984 Cj0984 hypothetical protein Cj0984 (NCBI ptt file) 50, 76
Cj0990c Cj0990c hypothetical protein Cj0990c (NCBI ptt file) 122, 164
Cj1010 tgt queuine tRNA-ribosyltransferase (NCBI ptt file) 56, 122
Cj1036c Cj1036c hypothetical protein Cj1036c (NCBI ptt file) 122, 167
Cj1042c Cj1042c putative transcriptional regulatory protein (NCBI ptt file) 50, 121
Cj1148 waaF ADP-heptose--LPS heptosyltransferase (NCBI ptt file) 50, 72
Cj1166c Cj1166c putative integral membrane protein (NCBI ptt file) 122, 149
Cj1219c Cj1219c putative periplasmic protein (NCBI ptt file) 50, 67
Cj1252 Cj1252 putative periplasmic protein (NCBI ptt file) 101, 122
Cj1302 Cj1302 hypothetical protein Cj1302 (NCBI ptt file) 122, 143
Cj1377c Cj1377c putative ferredoxin (NCBI ptt file) 50, 155
Cj1381 Cj1381 putative lipoprotein (NCBI ptt file) 70, 122
Cj1631c Cj1631c hypothetical protein Cj1631c (NCBI ptt file) 50, 75
Cj1726c metA putative homoserine O-succinyltransferase (NCBI ptt file) 50, 89
Cjp22 tRNA-Asn tRNA-Asn (NCBI) 4, 122
VIMSS46399 VIMSS46399 None 50, 117
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 Cj0480c
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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