Organism : Campylobacter jejuni | Module List :
hypothetical protein Cj0837c (NCBI ptt file)
Functional Annotations (5)
|nucleic acid binding||go/ molecular_function|
|ferrochelatase activity||go/ molecular_function|
|Porphyrin and chlorophyll metabolism||kegg/ kegg pathway|
|Metabolic pathways||kegg/ kegg pathway|
|Biosynthesis of secondary metabolites||kegg/ kegg pathway|
Regulation information for Cj0837c(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 Cj0837c
Module neighborhood information for Cj0837c
|Gene||Common Name||Description||Module membership|
|Cj0038c||Cj0038c||putative membrane protein (NCBI ptt file)||105, 152|
|Cj0122||Cj0122||hypothetical protein Cj0122 (NCBI ptt file)||22, 105|
|Cj0190c||Cj0190c||hypothetical protein Cj0190c (NCBI ptt file)||105, 152|
|Cj0266c||Cj0266c||putative integral membrane protein (NCBI ptt file)||53, 98|
|Cj0300c||modC||putative molybdenum transport ATP-binding protein (NCBI ptt file)||101, 105|
|Cj0342c||uvrA||excinuclease ABC subunit A (NCBI ptt file)||12, 105|
|Cj0402||glyA||serine hydroxymethyltransferase (NCBI ptt file)||53, 82|
|Cj0430||Cj0430||putative integral membrane protein (NCBI ptt file)||22, 105|
|Cj0489||ald'||putative aldehyde dehydrogenase N-terminus (RefSeq)||35, 53|
|Cj0506||alaS||alanyl-tRNA synthetase (NCBI ptt file)||10, 53|
|Cj0507||maf||MAF homolog (NCBI ptt file)||53, 157|
|Cj0525c||pbpB||putative penicillin-binding protein (NCBI ptt file)||53, 89|
|Cj0649||Cj0649||hypothetical protein Cj0649 (NCBI ptt file)||45, 105|
|Cj0680c||uvrB||excinuclease ABC subunit B (NCBI ptt file)||50, 53|
|Cj0681||Cj0681||hypothetical protein Cj0681 (NCBI ptt file)||53, 155|
|Cj0682||Cj0682||hypothetical protein Cj0682 (NCBI ptt file)||33, 53|
|Cj0832c||Cj0832c||putative integral membrane protein (NCBI ptt file)||53, 121|
|Cj0837c||Cj0837c||hypothetical protein Cj0837c (NCBI ptt file)||53, 105|
|Cj0839c||Cj0839c||hypothetical protein Cj0839c (NCBI ptt file)||10, 53|
|Cj0881c||Cj0881c||hypothetical protein Cj0881c (NCBI ptt file)||25, 53|
|Cj0924c||cheB'||putative MCP protein-glutamate methylesterase (NCBI ptt file)||53, 82|
|Cj0929||pepA||aminopeptidase (NCBI ptt file)||53, 137|
|Cj0970||Cj0970||hypothetical protein Cj0970 (NCBI ptt file)||105, 108|
|Cj1001||rpoD||RNA polymerase sigma factor (sigma-70) (NCBI ptt file)||53, 62|
|Cj1044c||thiH||thiH protein (NCBI ptt file)||49, 53|
|Cj1046c||moeB||putative molybdopterin biosynthesis protein (NCBI ptt file)||42, 53|
|Cj1051c||Cj1051c||restriction modification enzyme (NCBI ptt file)||58, 105|
|Cj1102||truB||tRNA pseudouridine synthase B (NCBI ptt file)||22, 105|
|Cj1201||metE||5-methyltetrahydropteroyltriglutamate--homocystei methyltransferase (NCBI ptt file)||25, 105|
|Cj1225||Cj1225||hypothetical protein Cj1225 (NCBI ptt file)||20, 53|
|Cj1264c||hydD||putative hydrogenase maturation protease (NCBI ptt file)||53, 162|
|Cj1279c||Cj1279c||putative fibronectin domain-containing lipoprotein (NCBI ptt file)||53, 74|
|Cj1321||Cj1321||putative transferase (NCBI ptt file)||101, 105|
|Cj1404||Cj1404||hypothetical protein Cj1404 (NCBI ptt file)||53, 152|
|Cj1410c||Cj1410c||putative membrane protein (NCBI ptt file)||25, 53|
|Cj1618c||Cj1618c||hypothetical protein Cj1618c (NCBI ptt file)||105, 108|
|Cj1649||Cj1649||putative lipoprotein (NCBI ptt file)||101, 105|
|Cj1653c||Cj1653c||probable lipoprotein (NCBI ptt file)||53, 144|
|Cj1674||Cj1674||hypothetical protein Cj1674 (NCBI ptt file)||53, 82|
|Cjp10||tRNA-Arg||tRNA-Arg (NCBI)||85, 105|
|Cjp13||tRNA-Gln||tRNA-Gln (NCBI)||5, 105|
|Cjp15||tRNA-Ile||tRNA-Ile (NCBI)||100, 105|
|Cjp16||tRNALeu||tRNA-Leu (RefSeq)||4, 105|
|Cjr03||rrf||5S ribosomal RNA (NCBI)||5, 105|
|Cjr05||rrl||23S ribosomal RNA (NCBI)||5, 105|
|Cjt4||tRNA-Arg||tRNA-Arg (NCBI)||30, 105|
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
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