Organism : Campylobacter jejuni | Module List :
Cj1546

hypothetical protein Cj1546 (NCBI ptt file)

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

Cytoscape Web
Regulation information for Cj1546
(Mouseover regulator name to see its description)

Cj1546 is regulated by 4 influences and regulates 2 modules.
Regulators for Cj1546 (4)
Regulator Module Operator
Cj0368c 56 tf
Cj0382c 56 tf
Cj0883c 56 tf
Cj1546 56 tf

Warning: Cj1546 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
7494 1.70e+03 AgCaaAGc
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7495 3.90e+03 cCCAaAAGCcCtAaaGGGc
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7698 6.00e+05 GcTAAAATCATAaC
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7699 3.50e+02 tCcaAAGc
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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 Cj1546

Cj1546 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for Cj1546

Cj1546 has total of 56 gene neighbors in modules 56, 158
Gene neighbors (56)
Gene Common Name Description Module membership
Cj0016 Cj0016 putative transcriptional regulatory protein (NCBI ptt file) 10, 158
Cj0138 Cj0138 hypothetical protein Cj0138 (NCBI ptt file) 11, 158
Cj0162c Cj0162c putative periplasmic protein (NCBI ptt file) 56, 81
Cj0238 Cj0238 putative integral membrane protein (NCBI ptt file) 56, 94
Cj0260c Cj0260c small hydrophobic protein (NCBI ptt file) 39, 158
Cj0272 Cj0272 hypothetical protein Cj0272 (NCBI ptt file) 39, 158
Cj0310c Cj0310c putative efflux protein (NCBI ptt file) 95, 158
Cj0355c Cj0355c two-component regulator (NCBI ptt file) 56, 170
Cj0366c Cj0366c transmembrane efflux protein (NCBI ptt file) 83, 158
Cj0374 Cj0374 hypothetical protein Cj0374 (NCBI ptt file) 13, 56
Cj0375 Cj0375 putative lipoprotein (NCBI ptt file) 13, 56
Cj0382c nusB transcription termination protein (NCBI ptt file) 52, 56
Cj0458c Cj0458c hypothetical protein Cj0458c (NCBI ptt file) 61, 158
Cj0463 Cj0463 zinc protease-like protein (NCBI ptt file) 56, 120
Cj0467 Cj0467 amino-acid ABC transporter integral membrane protein (NCBI ptt file) 56, 81
Cj0555 Cj0555 putative integral membrane protein (NCBI ptt file) 132, 158
Cj0607 Cj0607 ABC-type transmembrane transport protein (NCBI ptt file) 145, 158
Cj0620 Cj0620 hypothetical protein Cj0620 (NCBI ptt file) 76, 158
Cj0640c aspS aspartyl-tRNA synthetase (NCBI ptt file) 56, 170
Cj0643 Cj0643 putative two-component response regulator (NCBI ptt file) 34, 56
Cj0654c Cj0654c None 56, 132
Cj0668 Cj0668 putative ATP /GTP-binding protein (NCBI ptt file) 158, 160
Cj0704 glyQ glycyl-tRNA synthetase alpha chain (NCBI ptt file) 56, 158
Cj0824 uppS putative undecaprenyl diphosphate synthase (NCBI ptt file) 104, 158
Cj0864 Cj0864 putative periplasmic protein (NCBI ptt file) 119, 158
Cj0883c Cj0883c hypothetical protein Cj0883c (NCBI ptt file) 56, 114
Cj0884 rpsO 30S ribosomal protein S15 (NCBI ptt file) 26, 158
Cj0917c cstA carbon starvation protein A homolog (NCBI ptt file) 56, 158
Cj0969 Cj0969 None 47, 56
Cj1010 tgt queuine tRNA-ribosyltransferase (NCBI ptt file) 56, 122
Cj1084c Cj1084c putative ATP/GTP-binding protein (NCBI ptt file) 56, 65
Cj1173 Cj1173 putative efflux protein (NCBI ptt file) 123, 158
Cj1174 Cj1174 putative efflux protein (NCBI ptt file) 109, 158
Cj1216c Cj1216c hypothetical protein Cj1216c (NCBI ptt file) 26, 56
Cj1257c Cj1257c putative efflux pump (NCBI ptt file) 145, 158
Cj1277c Cj1277c putative ABC transporter ATP-binding protein (NCBI ptt file) 56, 69
Cj1306c Cj1306c hypothetical protein Cj1306c (617 family) (NCBI ptt file) 56, 120
Cj1320 Cj1320 putative aminotransferase (degT family) (NCBI ptt file) 56, 125
Cj1362 ruvB holliday junction DNA helicase (NCBI ptt file) 41, 56
Cj1374c Cj1374c hypothetical protein Cj1374c (NCBI ptt file) 148, 158
Cj1430c Cj1430c putative nucleotide-sugar epimerase/dehydratase (NCBI ptt file) 24, 158
Cj1454c Cj1454c hypothetical protein Cj1454c (NCBI ptt file) 125, 158
Cj1455 prfB peptide chain release factor 2 (NCBI ptt file) 56, 120
Cj1467 Cj1467 hypothetical protein Cj1467 (NCBI ptt file) 28, 56
Cj1503c putA putative proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI ptt file) 158, 165
Cj1532 Cj1532 possible periplasmic protein (NCBI ptt file) 81, 158
Cj1546 Cj1546 hypothetical protein Cj1546 (NCBI ptt file) 56, 158
Cj1580c Cj1580c putative peptide ABC-transport system ATP-binding protein (NCBI ptt file) 56, 128
Cj1583c Cj1583c putative peptide ABC-transport system permease protein (NCBI ptt file) 23, 56
Cj1584c Cj1584c putative peptide ABC-transport system periplasmic peptide-binding protein (NCBI ptt file) 56, 158
Cj1607 Cj1607 hypothetical protein Cj1607 (NCBI ptt file) 54, 158
Cj1610 pgpA putative phosphatidylglycerophosphatase (NCBI ptt file) 11, 158
Cj1633 Cj1633 hypothetical protein Cj1633 (NCBI ptt file) 51, 158
Cj1654c nhaA2 Na(+)/H(+) antiporter (NCBI ptt file) 132, 158
Cj1681c cysQ cysQ protein homolog (NCBI ptt file) 56, 120
VIMSS47265 VIMSS47265 None 56, 120
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 Cj1546
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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