Organism : Campylobacter jejuni | Module List :
Cj1556

hypothetical protein Cj1556 (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1556
(Mouseover regulator name to see its description)

Cj1556 is regulated by 2 influences and regulates 1 modules.
Regulators for Cj1556 (2)
Regulator Module Operator
Cj0757 58 tf
Cj1230 58 tf

Warning: Cj1556 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
7394 2.50e+03 GCTtCGCG
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7395 3.00e+03 TCcTAaaGCaTTg
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7498 4.40e+02 GAaGctacaaAAcgG
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7499 2.40e+02 ccTTaaagcaagaGggagAgtaGC
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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 Cj1556

Cj1556 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for Cj1556

Cj1556 has total of 43 gene neighbors in modules 6, 58
Gene neighbors (43)
Gene Common Name Description Module membership
Cj0030 Cj0030 hypothetical protein Cj0030 (NCBI ptt file) 58, 128
Cj0098 fmt methionyl-tRNA formyltransferase (NCBI ptt file) 58, 128
Cj0294 Cj0294 moeB/thiF family protein (NCBI ptt file) 6, 70
Cj0302c Cj0302c hypothetical protein Cj0302c (NCBI ptt file) 6, 150
Cj0307 bioA adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file) 21, 58
Cj0308c bioD putative dethiobiotin synthetase (NCBI ptt file) 6, 164
Cj0387 aroK shikimate kinase (NCBI ptt file) 6, 63
Cj0395c Cj0395c hypothetical protein Cj0395c (NCBI ptt file) 6, 35
Cj0556 Cj0556 hypothetical protein Cj0556 (NCBI ptt file) 6, 70
Cj0561c Cj0561c possible periplasmic protein (NCBI ptt file) 58, 148
Cj0577c queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI ptt file) 12, 58
Cj0598 Cj0598 putative membrane protein (NCBI ptt file) 25, 58
Cj0609c Cj0609c possible periplasmic protein (NCBI ptt file) 58, 70
Cj0651 Cj0651 putative integral membrane protein (NCBI ptt file) 6, 118
Cj0677 kdpB potassium-transporting ATPase B chain (NCBI ptt file) 12, 58
Cj0800c Cj0800c hypothetical protein Cj0800c (NCBI ptt file) 6, 19
Cj0808c Cj0808c small hydrophobic protein (NCBI ptt file) 6, 104
Cj0846 Cj0846 putative integral membrane protein (NCBI ptt file) 6, 70
Cj0847 psd putative phosphatidylserine decarboxylase (NCBI ptt file) 29, 58
Cj0848c Cj0848c hypothetical protein Cj0848c (NCBI ptt file) 6, 70
Cj0872 dsbA putative protein disulphide isomerase (NCBI ptt file) 49, 58
Cj0877c Cj0877c very hypothetical protein Cj0877c (NCBI ptt file) 44, 58
Cj0896c pheT phenylalanyl-tRNA synthetase beta chain (NCBI ptt file) 58, 133
Cj0910 Cj0910 putative periplasmic protein (NCBI ptt file) 58, 123
Cj0919c Cj0919c putative ABC-type amino-acid transporter permease protein (NCBI ptt file) 58, 91
Cj0945c Cj0945c putative helicase (NCBI ptt file) 37, 58
Cj1051c Cj1051c restriction modification enzyme (NCBI ptt file) 58, 105
Cj1055c Cj1055c putative integral membrane protein (NCBI ptt file) 6, 36
Cj1158c Cj1158c small hydrophobic protein (NCBI ptt file) 46, 58
Cj1160c Cj1160c small hydrophobic protein (NCBI ptt file) 58, 152
Cj1202 metF 5,10-methylenetetrahydrofolate reductase (NCBI ptt file) 6, 64
Cj1275c Cj1275c putative periplasmic protein (NCBI ptt file) 58, 167
Cj1283 ktrB putative K+ uptake protein (NCBI ptt file) 6, 72
Cj1284 ktrA putative K+ uptake protein (NCBI ptt file) 12, 58
Cj1361c Cj1361c hypothetical protein Cj1361c (NCBI ptt file) 6, 11
Cj1373 Cj1373 putative integral membrane protein (NCBI ptt file) 23, 58
Cj1442c Cj1442c hypothetical protein Cj1442c (NCBI ptt file) 6, 60
Cj1456c Cj1456c putative periplasmic protein (NCBI ptt file) 12, 58
Cj1504c selD putative selenide,water dikinase (NCBI ptt file) 58, 80
Cj1556 Cj1556 hypothetical protein Cj1556 (NCBI ptt file) 6, 58
Cj1602 Cj1602 hypothetical protein Cj1602 (NCBI ptt file) 29, 58
Cj1669c Cj1669c putative ATP-dependent DNA ligase (NCBI ptt file) 58, 66
VIMSS46212 VIMSS46212 None 6, 19
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 Cj1556
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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