Organism : Campylobacter jejuni | Module List :
putative ribosomal pseudouridine synthase (NCBI ptt file)
Functional Annotations (5)
|Pseudouridylate synthases, 23S RNA-specific||cog/ cog|
|pseudouridine synthesis||go/ biological_process|
|RNA binding||go/ molecular_function|
|pseudouridine synthase activity||go/ molecular_function|
Regulation information for Cj1280c(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for Cj1280c
Module neighborhood information for Cj1280c
|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
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.
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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.
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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.
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.
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CircVisOur 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)
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