Organism : Clostridium acetobutylicum | Module List :
Large subunit of NADH-dependent glutamate synthase (NCBI ptt file)
Functional Annotations (4)
|Glutamate synthase domain 2||cog/ cog|
|glutamate synthase (NADPH) activity||go/ molecular_function|
|glutamate biosynthetic process||go/ biological_process|
|glutamate synthase complex (NADPH)||go/ cellular_component|
Regulation information for CAC1673(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 CAC1673
Module neighborhood information for CAC1673
|Gene||Common Name||Description||Module membership|
|CAC0283||CAC0283||Molybdopterin biosynthesis protein (NCBI ptt file)||95, 290|
|CAC0469||spmA||Spore maturation protein A (gene spmA) (NCBI ptt file)||15, 290|
|CAC0601||CAC0601||Unchracterized membrane protein, possible permease (NCBI ptt file)||263, 330|
|CAC0737||CAC0737||NADP-specific glutamate dehydrogenase (NCBI ptt file)||45, 290|
|CAC0808||hybG||Hydrogenase expression factor (hybG) (NCBI ptt file)||95, 290|
|CAC0809||hypE||Hydrogenase formation factor (hypE) (NCBI ptt file)||95, 290|
|CAC1252||CAC1252||Possible membrane metalloendopeptidases (NCBI ptt file)||263, 330|
|CAC1673||gltA||Large subunit of NADH-dependent glutamate synthase (NCBI ptt file)||263, 290|
|CAC1713||CAC1713||Coat morphogenesis sporulation protein spoIVA (NCBI ptt file)||188, 290|
|CAC1864||CAC1864||Hypothetical protein (NCBI ptt file)||203, 290|
|CAC2059||CAC2059||Uncharacterized protein, YTFJ Bacillus subtilis ortholog (NCBI ptt file)||135, 290|
|CAC2088||CAC2088||Stage III sporulation protein AF, SpoIIIAF (NCBI ptt file)||17, 263|
|CAC2089||CAC2089||Stage III sporulation protein AE, SpoIIIAE (NCBI ptt file)||263, 279|
|CAC2090||CAC2090||Stage III sporulation protein AD, SpoIIIAD (NCBI ptt file)||17, 263|
|CAC2093||CAC2093||Stage III sporulation protein AA, SpoIIIAA (NCBI ptt file)||17, 263|
|CAC2416||CAC2416||Uncharacterized protein, ErfK family; contains peptidoglycan-binding domain (NCBI ptt file)||6, 263|
|CAC2426||CAC2426||Uncharacterized conserved protein (NCBI ptt file)||263, 330|
|CAC2427||CAC2427||Uncharacterized conserved protein (NCBI ptt file)||263, 330|
|CAC2428||CAC2428||Activator of 2-hydroxyglutaryl-CoA dehydratase (NCBI ptt file)||263, 330|
|CAC2616||CAC2616||Predicted iron-dependent transcription repressor (NCBI ptt file)||135, 290|
|CAC2859||spoIIID||Stage III sporulation protein D, SpoIIID (NCBI ptt file)||263, 364|
|CAC2860||CAC2860||Hypothetical protein (NCBI ptt file)||263, 364|
|CAC2861||spoIID||Sporulation protein SpoIID (NCBI ptt file)||263, 290|
|CAC2903||CAC2903||LysM domain containing membrane protein (NCBI ptt file)||263, 330|
|CAC2984||CAC2984||Hypothetical protein (NCBI ptt file)||188, 290|
|CAC3002||CAC3002||Uncharacterized consrved protein, YHJR B.subtilis family (NCBI ptt file)||203, 263|
|CAC3081||CAC3081||Spore-cortex-lytic enzyme, SLEB (NCBI ptt file)||203, 290|
|CAC3278||CAC3278||Uncharacterized protein, containing cell adhesion domain and ChW-repeats (NCBI ptt file)||263, 330|
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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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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