Organism : Clostridium acetobutylicum | Module List :
Uncharacterized protein, Yje/RRF2 family (NCBI ptt file)
Functional Annotations (2)
|Predicted transcriptional regulator||cog/ cog|
Regulation information for CAC0115(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 CAC0115
|Predicted transcriptional regulator||cog/ cog|
Module neighborhood information for CAC0115
|Gene||Common Name||Description||Module membership|
|CAC0034||CAC0034||Hypothetical protein (NCBI ptt file)||63, 298|
|CAC0115||CAC0115||Uncharacterized protein, Yje/RRF2 family (NCBI ptt file)||63, 232|
|CAC0207||CAC0207||Hypothetical protein, CF-6 family (NCBI ptt file)||63, 273|
|CAC0322||CAC0322||Sensory protein, containing EAL-domain (NCBI ptt file)||232, 295|
|CAC0493||CAC0493||Uncharcterized small conserved protein, YhhG family (NCBI ptt file)||64, 232|
|CAC0494||CAC0494||PemK family of DNA-binding proteins (NCBI ptt file)||32, 232|
|CAC0910||CAC0910||Probably cellulosomal scaffolding protein precursor, secreted; cellulose-binding and cohesin domain (NCBI ptt file)||53, 63|
|CAC0945||ssb||Single-stranded DNA-binding protein (NCBI ptt file)||63, 99|
|CAC1289||CAC1289||Uncharacterized conserved protein, YqeY B.subtilis ortholog (NCBI ptt file)||32, 232|
|CAC1313||CAC1313||Hypothetical protein (NCBI ptt file)||63, 295|
|CAC1488||CAC1488||Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file)||63, 273|
|CAC1745||rpmF||Ribosomal protein L32 (NCBI ptt file)||32, 232|
|CAC1747||acpA||Acyl carrier protein, ACP (NCBI ptt file)||32, 232|
|CAC1855||CAC1855||Hypothetical protein (NCBI ptt file)||63, 210|
|CAC1965||greA||Transcription elongation factor GreA (NCBI ptt file)||63, 109|
|CAC2072||CAC2072||Stage IV sporulation protein B, SpoIVB (NCBI ptt file)||63, 273|
|CAC2229||CAC2229||Pyruvate:ferredoxin oxidoreductase (NCBI ptt file)||59, 63|
|CAC2230||CAC2230||Uncharacterized protein of PR1 family, YkwD B.subtilis ortholog (NCBI ptt file)||63, 273|
|CAC2321||CAC2321||Predicted glycosyltransferase (NCBI ptt file)||63, 278|
|CAC2386||CAC2386||Predicted protein of beta-propeller fold (NCBI ptt file)||63, 321|
|CAC2711||bcd||Butyryl-CoA dehydrogenase (NCBI ptt file)||232, 255|
|CAC2712||crt||Crotonase (3-hydroxybutyryl-COA dehydratase) (NCBI ptt file)||61, 232|
|CAC2856||metK||S-adenosylmethionine synthetase (NCBI ptt file)||32, 232|
|CAC2858||mreV||Shape-determining protein envB (HSP70 family charepones) (NCBI ptt file)||36, 63|
|CAC2893||CAC2893||Hypothetical protein (NCBI ptt file)||63, 137|
|CAC2942||CAC2942||Uncharacterized conserved protein fron YGAG family, predicted metal-dependent enzyme (NCBI ptt file)||47, 63|
|CAC3135||CAC3135||Uncharacterized C4-type Zn-finger containing protein (NCBI ptt file)||232, 237|
|CAC3145||rplL||Ribosomal protein L7/L12 (NCBI ptt file)||61, 232|
|CAC3147||rplA||Ribosomal protein L1 (NCBI ptt file)||61, 232|
|CAC3150||secE||Preprotein translocase subunit SecE (NCBI ptt file)||116, 232|
|CAC3217||spoVC||Stage V sporulation protein C, peptidyl-tRNA hydrolase (NCBI ptt file)||63, 105|
|CAC3219||CAC3219||Membrane associated histidine kinase with HAMP domain (NCBI ptt file)||19, 63|
|CAC3224||purR||PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file)||232, 292|
|CAC3251||CAC3251||Sensory transduction protein containing HD_GYP domain (NCBI ptt file)||63, 225|
|CAC3252||proC||Pyrroline-5-carboxylate reductase (NCBI ptt file)||85, 232|
|CAC3394||CAC3394||Uncharacterized conserved protein, YGIN family (NCBI ptt file)||232, 292|
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
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.
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
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
- 6. Visualisation legend
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.