Organism : Campylobacter jejuni | Module List :
Cj0185c

phnA-like protein (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism cog/ cog
phosphonoacetate hydrolase activity go/ molecular_function
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0185c
(Mouseover regulator name to see its description)

Cj0185c is regulated by 1 influences and regulates 0 modules.
Regulators for Cj0185c (1)
Regulator Module Operator
Cj0571 7 tf

Warning: Cj0185c 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
7396 8.70e+03 cCAtAGGacAaCAAGaacCTG
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7397 1.80e+04 cCTTGCG
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7440 1.20e+02 aggGtAacgTtTtGG
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7441 2.10e+03 aAgCTttAgt
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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 Cj0185c

Cj0185c is enriched for 3 functions in 3 categories.
Module neighborhood information for Cj0185c

Cj0185c has total of 40 gene neighbors in modules 7, 29
Gene neighbors (40)
Gene Common Name Description Module membership
Cj0070c Cj0070c very hypothetical protein Cj0070c (NCBI ptt file) 29, 45
Cj0123c Cj0123c putative transcriptional regulator (NCBI ptt file) 17, 29
Cj0174c Cj0174c putative iron-uptake ABC transport system permease protein (NCBI ptt file) 7, 148
Cj0177 Cj0177 putative lipoprotein (NCBI ptt file) 7, 40
Cj0182 Cj0182 transmembrane transport protein (NCBI ptt file) 7, 33
Cj0185c Cj0185c phnA-like protein (NCBI ptt file) 7, 29
Cj0188c Cj0188c hypothetical protein Cj0188c (NCBI ptt file) 7, 47
Cj0255c Cj0255c exodeoxyribonuclease (NCBI ptt file) 7, 23
Cj0324 ubiE ubiquinonemenaquinone biosynthesis methlytransferase (VIMSS-AUTO) 7, 70
Cj0520 Cj0520 putative membrane protein (NCBI ptt file) 29, 108
Cj0571 Cj0571 putative transcriptional regulator (NCBI ptt file) 7, 167
Cj0613 pstS possible periplasmic phosphate binding protein (NCBI ptt file) 29, 78
Cj0614 pstC putative phosphate transport system permease protein (NCBI ptt file) 29, 78
Cj0635 Cj0635 hypothetical protein Cj0635 (NCBI ptt file) 7, 109
Cj0650 Cj0650 putative ATP /GTP binding protein (NCBI ptt file) 7, 17
Cj0801 Cj0801 integral membrane protein (MVIN homolog) (NCBI ptt file) 29, 41
Cj0804 pyrD dihydroorotate dehydrogenase (NCBI ptt file) 25, 29
Cj0809c Cj0809c putative hydrolase (NCBI ptt file) 11, 29
Cj0818 Cj0818 putative lipoprotein (NCBI ptt file) 29, 48
Cj0847 psd putative phosphatidylserine decarboxylase (NCBI ptt file) 29, 58
Cj0890c Cj0890c putative sensory transduction transcriptional regulator (NCBI ptt file) 7, 55
Cj0912c cysM cysteine synthase (NCBI ptt file) 7, 111
Cj0927 apt adenine phosphoribosyltransferase (NCBI ptt file) 29, 161
Cj0973 Cj0973 hypothetical protein Cj0973 (NCBI ptt file) 7, 141
Cj0974 Cj0974 very hypothetical protein Cj0974 (NCBI ptt file) 29, 62
Cj1095 Cj1095 putative integral membrane protein (NCBI ptt file) 7, 101
Cj1101 Cj1101 ATP-dependent DNA helicase (NCBI ptt file) 7, 96
Cj1157 dnaX putative DNA polymerase III subunit gamma (NCBI ptt file) 7, 19
Cj1162c Cj1162c hypothetical protein Cj1162c (NCBI ptt file) 7, 101
Cj1232 Cj1232 hypothetical protein Cj1232 (NCBI ptt file) 29, 64
Cj1247c Cj1247c hypothetical protein Cj1247c (NCBI ptt file) 7, 17
Cj1322 Cj1322 hypothetical protein Cj1322 (NCBI ptt file) 7, 101
Cj1354 ceuD enterochelin uptake ATP-binding protein (NCBI ptt file) 7, 121
Cj1394 Cj1394 putative fumarate lyase (NCBI ptt file) 7, 108
Cj1414c Cj1414c possible polysaccharide modification protein (NCBI ptt file) 7, 101
Cj1472c Cj1472c putative membrane protein (NCBI ptt file) 7, 104
Cj1565c pflA paralysed flagellum protein (NCBI ptt file) 7, 67
Cj1587c Cj1587c putative ABC transporter (NCBI ptt file) 7, 101
Cj1602 Cj1602 hypothetical protein Cj1602 (NCBI ptt file) 29, 58
Cj1646 iamB putative ABC transport system permease protein (NCBI ptt file) 7, 92
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 Cj0185c
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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