Organism : Campylobacter jejuni | Module List :
Cj0460 nusA

transcription termination factor (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0460
(Mouseover regulator name to see its description)

Cj0460 is regulated by 3 influences and regulates 4 modules.
Regulators for Cj0460 nusA (3)
Regulator Module Operator
Cj0287c 23 tf
Cj0757 23 tf
Cj1230 23 tf

Warning: Cj0460 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
7428 3.70e+00 AtCcACCCAtAaAGC
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7429 1.10e+03 AaAaTTtTaAGGAa
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7534 5.40e+03 CCGCaC
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7535 1.10e+04 GAAGGTcG
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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 Cj0460

Cj0460 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
Module neighborhood information for Cj0460

Cj0460 has total of 44 gene neighbors in modules 23, 76
Gene neighbors (44)
Gene Common Name Description Module membership
Cj0099 birA putative biotin--[acetyl-CoA-carboxylase] synthetase (NCBI ptt file) 23, 146
Cj0124c Cj0124c putative membrane protein (NCBI ptt file) 23, 141
Cj0125c Cj0125c dksA-like protein (NCBI ptt file) 17, 23
Cj0132 lpxC UDP-3-O-[3-hydroxymyristoyl] n-acetylglucosamine deacetylase (NCBI ptt file) 23, 61
Cj0134 thrB homoserine kinase (NCBI ptt file) 22, 23
Cj0181 tonB1 possible tonB transport protein (NCBI ptt file) 23, 51
Cj0184c Cj0184c possible serine 23, 101
Cj0189c Cj0189c hypothetical protein Cj0189c (NCBI ptt file) 76, 141
Cj0208 Cj0208 DNA modification methylase (adenine-specific methyltransferase) (NCBI ptt file) 76, 108
Cj0230c Cj0230c hypothetical protein Cj0230c (NCBI ptt file) 23, 101
Cj0250c Cj0250c putative transmembrane transport protein (NCBI ptt file) 76, 78
Cj0255c Cj0255c exodeoxyribonuclease (NCBI ptt file) 7, 23
Cj0258 Cj0258 putative helix-turn-helix motif protein (NCBI ptt file) 76, 150
Cj0267c Cj0267c putative integral membrane protein (NCBI ptt file) 12, 23
Cj0276 mreB homolog of E. coli rod shape-determining protein (NCBI ptt file) 76, 148
Cj0295 Cj0295 putative acetyltransferase (NCBI ptt file) 23, 26
Cj0432c murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI ptt file) 76, 104
Cj0460 nusA transcription termination factor (NCBI ptt file) 23, 76
Cj0503c hemH putative ferrochelatase (NCBI ptt file) 23, 96
Cj0522 Cj0522 putative membrane protein (NCBI ptt file) 23, 125
Cj0523 Cj0523 putative membrane protein (NCBI ptt file) 23, 101
Cj0546 Cj0546 hypothetical protein Cj0546 (NCBI ptt file) 23, 62
Cj0617 Cj0617 hypothetical protein Cj0617 (617 family) (NCBI ptt file) 23, 68
Cj0620 Cj0620 hypothetical protein Cj0620 (NCBI ptt file) 76, 158
Cj0648 Cj0648 hypothetical protein Cj0648 (NCBI ptt file) 70, 76
Cj0747 Cj0747 hypothetical protein Cj0747 (NCBI ptt file) 23, 96
Cj0849c Cj0849c hypothetical protein Cj0849c (NCBI ptt file) 23, 37
Cj0882c flhA flagellar biosynthesis protein (NCBI ptt file) 23, 143
Cj0904c Cj0904c putative RNA methylase (NCBI ptt file) 23, 27
Cj0952c Cj0952c putative membrane protein (NCBI ptt file) 23, 27
Cj0984 Cj0984 hypothetical protein Cj0984 (NCBI ptt file) 50, 76
Cj1079 Cj1079 putative periplasmic protein (NCBI ptt file) 76, 103
Cj1245c Cj1245c putative membrane protein (NCBI ptt file) 23, 96
Cj1254 Cj1254 hypothetical protein Cj1254 (NCBI ptt file) 23, 106
Cj1262 racS two-component sensor (histidine kinase) (NCBI ptt file) 23, 24
Cj1337 Cj1337 hypothetical protein Cj1337 (NCBI ptt file) 23, 134
Cj1373 Cj1373 putative integral membrane protein (NCBI ptt file) 23, 58
Cj1443c kpsF KpsF protein (NCBI ptt file) 23, 109
Cj1452 Cj1452 putative integral membrane protein (NCBI ptt file) 23, 89
Cj1473c Cj1473c putative ATP/GTP-binding protein (NCBI ptt file) 23, 96
Cj1481c Cj1481c putative helicase (NCBI ptt file) 23, 108
Cj1482c Cj1482c hypothetical protein Cj1482c (NCBI ptt file) 23, 37
Cj1552c Cj1552c hypothetical protein Cj1552c (NCBI ptt file) 76, 96
Cj1583c Cj1583c putative peptide ABC-transport system permease protein (NCBI ptt file) 23, 56
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 Cj0460
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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