Organism : Campylobacter jejuni | Module List :
Cj0101

parB family protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
parB_part tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0101
(Mouseover regulator name to see its description)

Cj0101 is regulated by 3 influences and regulates 4 modules.
Regulators for Cj0101 (3)
Regulator Module Operator
Cj0101 128 tf
Cj0473 128 tf
Cj1533c 128 tf

Warning: Cj0101 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
7434 2.10e+00 atttttAAGGAAAAa
Loader icon
7435 8.20e+02 GCCCTAGCC
Loader icon
7638 2.90e+02 GCaaGtGG
Loader icon
7639 6.70e+03 TcCCCC
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 Cj0101

Cj0101 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
parB_part tigr/ tigrfam
Module neighborhood information for Cj0101

Cj0101 has total of 57 gene neighbors in modules 26, 128
Gene neighbors (57)
Gene Common Name Description Module membership
Cj0030 Cj0030 hypothetical protein Cj0030 (NCBI ptt file) 58, 128
Cj0053c trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI ptt file) 26, 139
Cj0082 cydB cytochrome bd oxidase subunit II (NCBI ptt file) 44, 128
Cj0098 fmt methionyl-tRNA formyltransferase (NCBI ptt file) 58, 128
Cj0100 Cj0100 parA family protein (NCBI ptt file) 65, 128
Cj0101 Cj0101 parB family protein (NCBI ptt file) 26, 128
Cj0251c Cj0251c highly acidic protein (NCBI ptt file) 26, 90
Cj0263 Cj0263 putative integral membrane protein (NCBI ptt file) 66, 128
Cj0273 fabZ (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (NCBI ptt file) 26, 146
Cj0295 Cj0295 putative acetyltransferase (NCBI ptt file) 23, 26
Cj0334 ahpC alkyl hydroperoxide reductase (NCBI ptt file) 16, 128
Cj0443 accA acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (NCBI ptt file) 14, 26
Cj0504c Cj0504c hypothetical protein Cj0504c (NCBI ptt file) 48, 128
Cj0540 Cj0540 hypothetical protein Cj0540 (NCBI ptt file) 26, 89
Cj0586 ligA DNA ligase (NCBI ptt file) 26, 145
Cj0672 Cj0672 putative periplasmic protein (NCBI ptt file) 26, 137
Cj0777 Cj0777 putative ATP-dependent DNA helicase (NCBI ptt file) 26, 47
Cj0884 rpsO 30S ribosomal protein S15 (NCBI ptt file) 26, 158
Cj0886c ftsK putative cell division protein (NCBI ptt file) 26, 51
Cj0906c Cj0906c putative periplasmic protein (NCBI ptt file) 26, 84
Cj0954c Cj0954c putative dnaJ-like protein (NCBI ptt file) 26, 77
Cj0955c purL phosphoribosylformylglycinamidine synthase (NCBI ptt file) 19, 26
Cj0958c Cj0958c putative membrane protein (NCBI ptt file) 26, 47
Cj0981c Cj0981c transmembrane transport protein (NCBI ptt file) 26, 47
Cj0986c Cj0986c putative integral membrane protein (NCBI ptt file) 26, 133
Cj1013c Cj1013c putative membrane protein (NCBI ptt file) 128, 151
Cj1014c livF branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) 128, 151
Cj1016c livM putative branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) 104, 128
Cj1017c livH branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) 128, 151
Cj1019c livJ branched-chain amino-acid ABC transport system periplasmic binding protein (NCBI ptt file) 61, 128
Cj1033 Cj1033 putative integral membrane component of efflux system (NCBI ptt file) 117, 128
Cj1057c Cj1057c putative coiled-coil protein (NCBI ptt file) 25, 26
Cj1163c Cj1163c putative cation transport protein (NCBI ptt file) 51, 128
Cj1180c Cj1180c putative ABC transporter ATP binding protein (NCBI ptt file) 26, 62
Cj1194 Cj1194 possible phosphate permease (NCBI ptt file) 26, 129
Cj1208 Cj1208 hypothetical protein Cj1208 (NCBI ptt file) 92, 128
Cj1210 Cj1210 putative integral membrane protein (NCBI ptt file) 26, 54
Cj1216c Cj1216c hypothetical protein Cj1216c (NCBI ptt file) 26, 56
Cj1217c Cj1217c hypothetical protein Cj1217c (NCBI ptt file) 26, 148
Cj1256c Cj1256c putative membrane protein (NCBI ptt file) 26, 52
Cj1282 mrdB RodA protein homolog (NCBI ptt file) 26, 141
Cj1375 Cj1375 putative efflux protein (NCBI ptt file) 128, 148
Cj1385 katA catalase (NCBI ptt file) 16, 128
Cj1437c Cj1437c putative aminotransferase (NCBI ptt file) 26, 125
Cj1440c Cj1440c putative sugar transferase (NCBI ptt file) 128, 141
Cj1479c rpsI 30S ribosomal protein S9 (NCBI ptt file) 111, 128
Cj1483c Cj1483c putative lipoprotein (NCBI ptt file) 26, 44
Cj1533c Cj1533c putative helix-turn-helix containsing protein (NCBI ptt file) 109, 128
Cj1567c nuoM NADH dehydrogenase I chain M (NCBI ptt file) 26, 166
Cj1580c Cj1580c putative peptide ABC-transport system ATP-binding protein (NCBI ptt file) 56, 128
Cj1670c Cj1670c putative periplasmic protein (NCBI ptt file) 128, 141
Cj1675 fliQ flagellar biosynthetic protein (NCBI ptt file) 26, 133
Cj1688c secY preprotein translocase subunit (NCBI ptt file) 128, 151
Cj1689c rplO 50S ribosomal protein L15 (NCBI ptt file) 128, 138
Cj1709c Cj1709c putative ribosomal pseudouridine synthase (NCBI ptt file) 128, 141
Cj1710c Cj1710c hypothetical protein Cj1710c (NCBI ptt file) 128, 151
Cj1711c ksgA putative dimethyladenosine transferase (16S rRNA dimethylase) (NCBI ptt file) 128, 151
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 Cj0101
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