Organism : Campylobacter jejuni | Module List :
hypothetical protein Cj1254 (NCBI ptt file)
Functional Annotations (1)
|G:T/U mismatch-specific DNA glycosylase||cog/ cog|
Regulation information for Cj1254(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 Cj1254
|G:T/U mismatch-specific DNA glycosylase||cog/ cog|
Module neighborhood information for Cj1254
|Gene||Common Name||Description||Module membership|
|Cj0031||Cj0031||putative type IIS restriction/modification enzyme (NCBI)||106, 141|
|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|
|Cj0230c||Cj0230c||hypothetical protein Cj0230c (NCBI ptt file)||23, 101|
|Cj0255c||Cj0255c||exodeoxyribonuclease (NCBI ptt file)||7, 23|
|Cj0267c||Cj0267c||putative integral membrane protein (NCBI ptt file)||12, 23|
|Cj0295||Cj0295||putative acetyltransferase (NCBI ptt file)||23, 26|
|Cj0335||flhB||flagellar biosynthetic protein (NCBI ptt file)||106, 129|
|Cj0386||Cj0386||putative GTP-binding protein (NCBI ptt file)||36, 106|
|Cj0460||nusA||transcription termination factor (NCBI ptt file)||23, 76|
|Cj0464||recG||ATP-dependent DNA helicase (NCBI ptt file)||12, 106|
|Cj0499||Cj0499||HIT-like protein (NCBI ptt file)||106, 133|
|Cj0500||Cj0500||putative ATP /GTP binding protein (NCBI ptt file)||51, 106|
|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|
|Cj0569||Cj0569||hypothetical protein Cj0569 (NCBI ptt file)||51, 106|
|Cj0617||Cj0617||hypothetical protein Cj0617 (617 family) (NCBI ptt file)||23, 68|
|Cj0634||Cj0634||SMF family protein (NCBI ptt file)||106, 109|
|Cj0739||Cj0739||hypothetical protein Cj0739 (NCBI ptt file)||106, 116|
|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|
|Cj1043c||Cj1043c||possible transferase (NCBI ptt file)||43, 106|
|Cj1047c||Cj1047c||hypothetical protein Cj1047c (NCBI ptt file)||43, 106|
|Cj1048c||dapE||succinyl-diaminopimelate desuccinylase (NCBI ptt file)||51, 106|
|Cj1125c||wlaG||putative galactosyltransferase (NCBI ptt file)||106, 109|
|Cj1236||Cj1236||hypothetical protein Cj1236 (NCBI ptt file)||72, 106|
|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|
|Cj1263||recR||recombination protein (NCBI ptt file)||70, 106|
|Cj1303||fabH2||putative 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file)||106, 141|
|Cj1337||Cj1337||hypothetical protein Cj1337 (NCBI ptt file)||23, 134|
|Cj1343c||Cj1343c||putative periplasmic protein (NCBI ptt file)||92, 106|
|Cj1353||ceuC||enterochelin uptake permease (NCBI ptt file)||3, 106|
|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|
|Cj1517||moaD||possible molybdopterin converting factor, subunit 1 (NCBI ptt file)||98, 106|
|Cj1519||moeA2||putative molybdopterin biosynthesis protein (NCBI ptt file)||80, 106|
|Cj1583c||Cj1583c||putative peptide ABC-transport system permease protein (NCBI ptt file)||23, 56|
|Cj1667c||Cj1667c||repA protein homolog (NCBI ptt file)||106, 129|
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.
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.
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)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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