Organism : Clostridium acetobutylicum | Module List :
Prolyl-tRNA synthetase (NCBI ptt file)
Functional Annotations (6)
|Prolyl-tRNA synthetase||cog/ cog|
|proline-tRNA ligase activity||go/ molecular_function|
|ATP binding||go/ molecular_function|
|prolyl-tRNA aminoacylation||go/ biological_process|
Regulation information for CAC3178(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 CAC3178
Module neighborhood information for CAC3178
|Gene||Common Name||Description||Module membership|
|CAC0095||hemA||Glutamil-tRNA reductase (NCBI ptt file)||92, 191|
|CAC0096||hemW||Precorrin-2 dehydrogenase (NCBI ptt file)||92, 191|
|CAC0097||hemC||Hydroxymrthylbilane syntase (porphobilinogen deaminase) (NCBI ptt file)||92, 191|
|CAC0098||hemD||Uroporphyrinogen III syntase (NCBI ptt file)||92, 191|
|CAC0099||hemL||Glutamate-1-semialdehyde aminotransferase (NCBI ptt file)||92, 191|
|CAC0100||hemB||Delta-aminolevulinic acid dehydratase (porphobilinogen synthase) (NCBI ptt file)||92, 191|
|CAC0167||CAC0167||Possible sigma factor, diverged member of sigF/sigE/sigG family (NCBI ptt file)||191, 223|
|CAC0293||CAC0293||MccF-like protein (NCBI ptt file)||49, 191|
|CAC0306||CAC0306||SAM-dependent methyltransferase (NCBI ptt file)||217, 353|
|CAC0307||CAC0307||Predicted methyltransferase (NCBI ptt file)||191, 217|
|CAC0332||manB||Beta-mannanase (NCBI ptt file)||191, 301|
|CAC0415||CAC0415||TPR-repeat-containing protein (NCBI ptt file)||151, 217|
|CAC0416||CAC0416||TPR-repeat-containing protein (NCBI ptt file)||151, 217|
|CAC0517||pfk||6-phosphofructokinase (NCBI ptt file)||10, 191|
|CAC0518||pykA||Pyruvate kinase (pykA) (NCBI ptt file)||191, 242|
|CAC0571||CAC0571||Predicted transcriptional regulator (NCBI ptt file)||191, 353|
|CAC0572||CAC0572||Predicted membrane protein (NCBI ptt file)||191, 353|
|CAC0628||CAC0628||Putative Mn transporter, NRAMR family (NCBI ptt file)||191, 207|
|CAC0698||CAC0698||Predicted hydrolase of the HAD superfamily (NCBI ptt file)||217, 351|
|CAC0699||CAC0699||Spore photoproduct lyase, splB (NCBI ptt file)||9, 217|
|CAC0908||CAC0908||Dinucleotide-utilizing enzyme involved in molybdopterin and thiamine biosynthesis family 1 (NCBI ptt file)||217, 324|
|CAC1485||CAC1485||Glycosyltransferase, involved in cell wall biogenesis (NCBI ptt file)||191, 298|
|CAC1690||pilT||PilT ATPase involved in pili biogenesis (NCBI ptt file)||92, 217|
|CAC1972||CAC1972||Predicted membrane protein (NCBI ptt file)||191, 351|
|CAC2166||CAC2166||Nucleoside-diphosphate-sugar epimerase (NCBI ptt file)||96, 217|
|CAC2523||CAC2523||Glycosyltransferase (NCBI ptt file)||191, 359|
|CAC2524||CAC2524||Uncharacterized conserved membrane protein (NCBI ptt file)||107, 191|
|CAC2526||CAC2526||6-pyruvoyl-tetrahydropterin synthase related protein (NCBI ptt file)||9, 191|
|CAC3177||cysS||Cysteinyl-tRNA synthetase (NCBI ptt file)||191, 217|
|CAC3178||proS||Prolyl-tRNA synthetase (NCBI ptt file)||191, 217|
|CAC3352||CAC3352||Membrane associated methyl-accepting chemotaxis protein with HAMP domain (NCBI ptt file)||151, 217|
|CAC3492||CAC3492||Uncharacterized conserved protein (NCBI ptt file)||205, 217|
|CAC3517||CAC3517||Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||217, 326|
|CAC3544||CAC3544||Membrane associated GGDEF domain containing protein (NCBI ptt file)||191, 217|
|CAC3545||CAC3545||Methyl-accepting chemotaxis protein (NCBI ptt file)||191, 217|
|CAC3642||CAC3642||Oligopeptide ABC transporter, ATPase component (NCBI ptt file)||65, 217|
|CAC3643||CAC3643||Oligopeptide ABC transporter, permease component (NCBI ptt file)||43, 217|
|CAC3644||CAC3644||Oligopeptide ABC transporter, permease component (NCBI ptt file)||217, 301|
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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