Organism : Campylobacter jejuni | Module List :
Cj1280c

putative ribosomal pseudouridine synthase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1280c
(Mouseover regulator name to see its description)

Cj1280c is regulated by 4 influences and regulates 0 modules.
Regulators for Cj1280c (4)
Regulator Module Operator
Cj0473 14 tf
Cj0479 14 tf
Cj0480c 14 tf
Cj1595 14 tf

Warning: Cj1280c 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
7410 4.70e+03 GcTacaACcaTAaAGCaCCG
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7411 1.60e+02 AGtaAAAttaagttAAAAttg
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7576 1.30e+03 GGTGcGc
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7577 1.00e+04 GCAAAaTAAGcacGc
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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 Cj1280c

Cj1280c is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for Cj1280c

Cj1280c has total of 41 gene neighbors in modules 14, 97
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0092 Cj0092 putative periplasmic protein (NCBI ptt file) 90, 97
Cj0094 rplU 50S ribosomal protein L21 (NCBI ptt file) 14, 111
Cj0095 rpmA 50S ribosomal protein L27 (NCBI ptt file) 14, 83
Cj0129c Cj0129c outer membrane protein (NCBI ptt file) 14, 133
Cj0154c Cj0154c putative methylase (NCBI ptt file) 14, 151
Cj0155c rpmE 50S ribosomal protein L31 (NCBI ptt file) 14, 123
Cj0274 lpxA acyl-[acyl-carrier-protein]--UDP-N-acetylglucosam O-acyltransferase (NCBI ptt file) 14, 61
Cj0275 clpX ATP-dependent clp protease ATP-binding subunit clpX (NCBI ptt file) 14, 151
Cj0330c rpmF 50S ribosomal protein L32 (NCBI ptt file) 14, 151
Cj0443 accA acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (NCBI ptt file) 14, 26
Cj0472 secE preprotein translocase SecE subunit (NCBI ptt file) 14, 163
Cj0473 nusG putative transcription antitermination protein (NCBI ptt file) 14, 163
Cj0474 rplK 50S ribosomal protein L11 (NCBI ptt file) 14, 163
Cj0475 rplA 50S ribosomal protein L1 (NCBI ptt file) 14, 163
Cj0476 rplJ 50S ribosomal protein L10 (NCBI ptt file) 14, 163
Cj0477 rplL 50S ribosomal protein L7 /L12 (NCBI ptt file) 14, 42
Cj0694 Cj0694 putative periplasmic protein (NCBI ptt file) 14, 118
Cj0703 Cj0703 hypothetical protein Cj0703 (NCBI ptt file) 14, 141
Cj0710 rpsP 30S ribosomal protein S16 (NCBI ptt file) 97, 99
Cj0711 Cj0711 hypothetical protein Cj0711 (NCBI ptt file) 8, 97
Cj0721c Cj0721c putative integral membrane protein (NCBI ptt file) 97, 144
Cj0873c Cj0873c hypothetical protein Cj0873c (NCBI ptt file) 97, 145
Cj0876c Cj0876c putative periplasmic protein (NCBI ptt file) 90, 97
Cj0900c Cj0900c small hydrophobic protein (NCBI ptt file) 14, 66
Cj0921c peb1A probable ABC-type amino-acid transporter periplasmic solute-binding protein (NCBI ptt file) 97, 135
Cj1092c secF protein-export membrane protein (NCBI ptt file) 14, 111
Cj1093c secD protein-export membrane protein (NCBI ptt file) 14, 133
Cj1106 Cj1106 possible periplasmic thioredoxin (NCBI ptt file) 14, 98
Cj1280c Cj1280c putative ribosomal pseudouridine synthase (NCBI ptt file) 14, 97
Cj1324 Cj1324 hypothetical protein Cj1324 (NCBI ptt file) 97, 117
Cj1366c glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI ptt file) 97, 111
Cj1407c Cj1407c putative phospho-sugar mutase (NCBI ptt file) 14, 111
Cj1441c kfiD putative UDP-glucose 6-dehydrogenase (NCBI ptt file) 14, 137
Cj1491c Cj1491c putative two-component regulator (NCBI ptt file) 8, 97
Cj1493c Cj1493c putative integral membrane protein (NCBI ptt file) 3, 97
Cj1495c Cj1495c hypothetical protein Cj1495c (NCBI ptt file) 14, 98
Cj1505c Cj1505c hypothetical protein Cj1505c (NCBI ptt file) 11, 97
Cj1540 Cj1540 putative periplasmic protein (NCBI ptt file) 14, 123
Cj1595 rpoA DNA-directed RNA polymerase alpha chain (NCBI ptt file) 14, 30
Cj1611 rpsT 30S ribosomal protein S20 (NCBI ptt file) 14, 141
Cj1696c rplX 50S ribosomal protein L24 (NCBI ptt file) 14, 163
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 Cj1280c
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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