Organism : Bacillus subtilis | Module List :
BSU31930 ald

L-alanine dehydrogenase (RefSeq)

CircVis
Functional Annotations (8)
Function System
Alanine dehydrogenase cog/ cog
alanine dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
potassium ion transport go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Taurine and hypotaurine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
alaDH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU31930
(Mouseover regulator name to see its description)

BSU31930 is regulated by 30 influences and regulates 0 modules.
Regulators for BSU31930 ald (30)
Regulator Module Operator
BSU05370 256 tf
BSU05670 256 tf
BSU09990 256 tf
BSU10560 256 tf
BSU13150 256 tf
BSU14140 256 tf
BSU16900 256 tf
BSU19200 256 tf
BSU23120 256 tf
BSU23520 256 tf
BSU26430 256 tf
BSU28820 256 tf
BSU35080 256 tf
BSU40970 256 tf
BSU00330 90 tf
BSU02680 90 tf
BSU04820 90 tf
BSU05270 90 tf
BSU05670 90 tf
BSU09990 90 tf
BSU13870 90 tf
BSU20780 90 tf
BSU25200 90 tf
BSU27520 90 tf
BSU29690 90 tf
BSU35490 90 tf
BSU35650 90 tf
BSU36110 90 tf
BSU39990 90 tf
BSU40970 90 tf

Warning: BSU31930 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5134 1.60e+01 AgGAGagg
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5135 2.10e+02 AaaacGaAagaGctt
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5452 5.10e-02 GaAaAcgCTTtC
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5453 2.40e-02 gaGGaaGaGa
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BSU31930

BSU31930 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Alanine dehydrogenase cog/ cog
alanine dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
potassium ion transport go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Taurine and hypotaurine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
alaDH tigr/ tigrfam
Module neighborhood information for BSU31930

BSU31930 has total of 50 gene neighbors in modules 90, 256
Gene neighbors (50)
Gene Common Name Description Module membership
BSU03410 bglC aryl-phospho-beta-d-glucosidase (RefSeq) 90, 217
BSU03480 srfAA surfactin synthetase (RefSeq) 90, 353
BSU03490 srfAB surfactin synthetase (RefSeq) 90, 353
BSU03500 comS regulator of genetic competence (RefSeq) 90, 353
BSU03510 srfAC surfactin synthetase (RefSeq) 90, 353
BSU03520 srfAD surfactin synthetase (RefSeq) 90, 353
BSU03770 rapC response regulator aspartate phosphatase (RefSeq) 90, 353
BSU03990 mtlD mannitol-1-phosphate 5-dehydrogenase (RefSeq) 90, 330
BSU06240 test acetoin reductase/2,3-butanediol dehydrogenase (RefSeq) 90, 340
BSU07450 yfmJ putative oxidoreductase (RefSeq) 90, 359
BSU08470 yfhB putative isomerase (RefSeq) 90, 353
BSU09420 lytE cell wall hydrolase; phosphatase-associated protein (major autolysin) (RefSeq) 169, 256
BSU10020 serC phosphoserine aminotransferase (RefSeq) 247, 256
BSU10210 yhfF hypothetical protein (RefSeq) 90, 101
BSU10850 yisS putative dehydrogenase (RefSeq) 256, 340
BSU11540 pepF oligoendopeptidase F (RefSeq) 90, 412
BSU16090 sucC succinyl-CoA synthetase subunit beta (RefSeq) 169, 256
BSU16100 sucD succinyl-CoA synthetase subunit alpha (RefSeq) 169, 256
BSU18630 exlX extracellular endoglucanase precursor (expansin) (RefSeq) 25, 90
BSU19360 odhB dihydrolipoamide succinyltransferase (RefSeq) 169, 256
BSU19370 sucA 2-oxoglutarate dehydrogenase E1 component (RefSeq) 169, 256
BSU22730 ndk nucleoside diphosphate kinase (RefSeq) 105, 256
BSU22960 gudB cryptic glutamate dehydrogenase (RefSeq) 169, 256
BSU23130 resC factor required for cytochrome c synthesis (RefSeq) 256, 340
BSU23140 resB factor required for cytochrome c synthesis (RefSeq) 256, 340
BSU23150 resA thiol-disulfide oxidoreductase (RefSeq) 256, 340
BSU24460 yqhT putative aminopeptidase (RefSeq) 247, 256
BSU24470 yqhS 3-dehydroquinate dehydratase (RefSeq) 29, 256
BSU28440 sdhA succinate dehydrogenase flavoprotein subunit (RefSeq) 169, 256
BSU28450 sdhC succinate dehydrogenase (cytochrome b558 subunit) (RefSeq) 169, 256
BSU29120 mdh malate dehydrogenase (RefSeq) 169, 256
BSU29130 icd isocitrate dehydrogenase (RefSeq) 169, 256
BSU29140 citZ citrate synthase (RefSeq) 169, 256
BSU29670 tyrS tyrosyl-tRNA synthetase (RefSeq) 90, 340
BSU29950 ytlQ putative hydrolase (RefSeq) 169, 256
BSU29960 ytlP 2'-5' RNA-ligase family protein (RefSeq) 169, 256
BSU31690 comP two-component sensor histidine kinase (RefSeq) 90, 340
BSU31700 comX competence pheromone precursor (pheromone peptide aa 46->55, modified) (RefSeq) 90, 340
BSU31930 ald L-alanine dehydrogenase (RefSeq) 90, 256
BSU33540 yvaB azoreductase (RefSeq) 90, 353
BSU34030 yvbY putative subunit of an iron-sulfur protein (RefSeq) 63, 256
BSU34040 yvfW putative iron-sulfur oxidoreductase (RefSeq) 63, 256
BSU34050 yvfV putative iron-sulfur heterodisulfide reductase (RefSeq) 169, 256
BSU34630 mdxR putative transcriptional regulator (LacI family) (RefSeq) 90, 318
BSU35890 pgsC capsular polyglutamate amide ligase/translocase subunit (RefSeq) 61, 90
BSU35900 pgsB capsular polyglutamate synthetase (ATP-dependent amide ligase) (RefSeq) 61, 90
BSU37660 eutD phosphotransacetylase (RefSeq) 247, 256
BSU39090 yxiP putative lipoprotein (RefSeq) 90, 91
BSU39820 htpG heat shock protein 90 (RefSeq) 90, 229
VIMSS39309 VIMSS39309 None 90, 191
Gene Page Help

Network Tab

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

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.

Motifs Tab

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.

Functions Tab

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.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

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.

CircVis

Our 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
Comments for BSU31930
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our 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