Organism : Campylobacter jejuni | Module List :
Cj1561

putative transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1561
(Mouseover regulator name to see its description)

Cj1561 is regulated by 8 influences and regulates 4 modules.
Regulators for Cj1561 (8)
Regulator Module Operator
Cj0287c 40 tf
Cj0368c 40 tf
Cj0400 40 tf
Cj0466 40 tf
Cj0571 40 tf
Cj0757 40 tf
Cj1024c 40 tf
Cj1561 40 tf

Warning: Cj1561 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
7462 3.50e+03 TCGCCc
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7463 1.30e+04 CTTcCaaGTGAC
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7484 1.10e+04 CGAGGAC
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7485 6.80e+02 .CTcgc.g.Gg
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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 Cj1561

Cj1561 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for Cj1561

Cj1561 has total of 41 gene neighbors in modules 40, 51
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0001 dnaA chromosomal replication initiator protein (NCBI ptt file) 51, 89
Cj0054c Cj0054c hypothetical protein Cj0054c (NCBI ptt file) 51, 148
Cj0140 Cj0140 hypothetical protein Cj0140 (NCBI ptt file) 40, 101
Cj0145 Cj0145 hypothetical protein Cj0145 (NCBI ptt file) 40, 131
Cj0173c Cj0173c putative iron-uptake ABC transport system ATP-binding protein (NCBI ptt file) 40, 143
Cj0177 Cj0177 putative lipoprotein (NCBI ptt file) 7, 40
Cj0181 tonB1 possible tonB transport protein (NCBI ptt file) 23, 51
Cj0183 Cj0183 putative integral membrane protein with haemolysin domain (NCBI ptt file) 51, 78
Cj0247c Cj0247c hypothetical protein Cj0247c (NCBI ptt file) 37, 51
Cj0262c Cj0262c putative methyl-accepting chemotaxis signal transduction protein (NCBI ptt file) 40, 156
Cj0280 Cj0280 hypothetical protein Cj0280 (NCBI ptt file) 51, 70
Cj0379c Cj0379c hypothetical protein Cj0379c (NCBI ptt file) 40, 107
Cj0452 dnaQ exonuclease, possibly dna polymerase III epsilon subunit (NCBI ptt file) 51, 98
Cj0500 Cj0500 putative ATP /GTP binding protein (NCBI ptt file) 51, 106
Cj0569 Cj0569 hypothetical protein Cj0569 (NCBI ptt file) 51, 106
Cj0667 Cj0667 hypothetical protein Cj0667 (NCBI ptt file) 51, 61
Cj0712 rimM putative 16S rRNA processing protein (NCBI ptt file) 34, 51
Cj0753c tonB3 tonB transport protein (NCBI ptt file) 33, 51
Cj0831c trmA tRNA (uracil-5-)-methyltransferase (NCBI ptt file) 45, 51
Cj0886c ftsK putative cell division protein (NCBI ptt file) 26, 51
Cj0915 Cj0915 putative hydrolase (NCBI ptt file) 33, 40
Cj0975 Cj0975 putative outer-membrane protein (NCBI ptt file) 12, 51
Cj0991c Cj0991c putative oxidoreductase ferredoxin-type electron transport protein (NCBI ptt file) 51, 113
Cj1048c dapE succinyl-diaminopimelate desuccinylase (NCBI ptt file) 51, 106
Cj1049c Cj1049c putative integral membrane protein (NCBI ptt file) 39, 51
Cj1050c Cj1050c putative transferase (NCBI ptt file) 51, 121
Cj1052c mutS putative mismatch repair protein (NCBI ptt file) 21, 51
Cj1053c Cj1053c putative integral membrane protein (NCBI ptt file) 41, 51
Cj1143 neuA1 acylneuraminate cytidylyltransferase (NCBI ptt file) 40, 101
Cj1156 rho transcription termination factor (NCBI ptt file) 51, 166
Cj1161c Cj1161c putative cation-transporting ATPase (NCBI ptt file) 51, 57
Cj1163c Cj1163c putative cation transport protein (NCBI ptt file) 51, 128
Cj1206c ftsY putative signal recognition particle protein (NCBI ptt file) 51, 116
Cj1207c Cj1207c putative lipoprotein thiredoxin (NCBI ptt file) 51, 165
Cj1235 Cj1235 putative periplasmic protein (NCBI ptt file) 40, 149
Cj1272c spoT putative guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (NCBI ptt file) 25, 51
Cj1310c Cj1310c hypothetical protein Cj1310c (617 family) (NCBI ptt file) 51, 77
Cj1386 Cj1386 ankyrin-repeat containing protein (NCBI ptt file) 2, 40
Cj1561 Cj1561 putative transcriptional regulator (NCBI ptt file) 40, 51
Cj1630 tonB2 putative tonB transport protein (NCBI ptt file) 40, 143
Cj1633 Cj1633 hypothetical protein Cj1633 (NCBI ptt file) 51, 158
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 Cj1561
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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