Organism : Bacillus subtilis | Module List :
BSU16960 ymdA

phosphodiesterase (RefSeq)

CircVis
Functional Annotations (4)
Function System
HD-GYP domain cog/ cog
RNA binding go/ molecular_function
catalytic activity go/ molecular_function
HDIG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16960
(Mouseover regulator name to see its description)

BSU16960 is regulated by 20 influences and regulates 0 modules.
Regulators for BSU16960 ymdA (20)
Regulator Module Operator
BSU00800 107 tf
BSU03080 107 tf
BSU03960 107 tf
BSU11660 107 tf
BSU15880 107 tf
BSU30460 107 tf
BSU33030 107 tf
BSU34380 107 tf
BSU35520 107 tf
BSU36020 107 tf
BSU36300 107 tf
BSU39770 107 tf
BSU01010 266 tf
BSU04650 266 tf
BSU09510 266 tf
BSU13210 266 tf
BSU23090 266 tf
BSU28410 266 tf
BSU35840 266 tf
BSU37160 266 tf

Warning: BSU16960 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
5168 2.30e-01 AAaagGaggtGaaat
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5169 1.50e+03 GccCTtGTC
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5472 2.20e+02 ggaGGAGGtGaaAg
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5473 3.70e+04 AgAaAGGgaGtggCa
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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 BSU16960

BSU16960 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
HD-GYP domain cog/ cog
RNA binding go/ molecular_function
catalytic activity go/ molecular_function
HDIG tigr/ tigrfam
Module neighborhood information for BSU16960

BSU16960 has total of 52 gene neighbors in modules 107, 266
Gene neighbors (52)
Gene Common Name Description Module membership
BSU03370 yckA putative ABC transporter (permease) (RefSeq) 98, 266
BSU03380 yckB putative ABC transporter (binding lipoprotein) (RefSeq) 98, 266
BSU03800 yclN putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03810 yclO putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03820 yclP putative iron-siderophore ABC transporter (ATP-binding protein) (RefSeq) 93, 266
BSU03830 yclQ putative iron-siderophore ABC transporter (binding lipoprotein) (RefSeq) 93, 266
BSU04580 cshA ATP-dependent RNA helicase; cold shock (RefSeq) 266, 322
BSU04650 endB antitoxin MazF (RefSeq) 212, 266
BSU04660 ndoA endoribonuclease toxin (RefSeq) 212, 266
BSU05480 ydfN putative oxidoreductase (RefSeq) 107, 178
BSU06270 ydjO hypothetical protein (RefSeq) 159, 266
BSU09100 cspB major cold-shock protein, RNA helicase co-factor, RNA co-chaperone (RefSeq) 266, 322
BSU12260 yjlA putative permease (RefSeq) 107, 132
BSU12280 rex transcriptional repressor of the rex ndh operon (RefSeq) 119, 266
BSU12290 ndh NADH dehydrogenase (RefSeq) 119, 266
BSU16960 ymdA phosphodiesterase (RefSeq) 107, 266
BSU17790 yndH hypothetical protein (RefSeq) 107, 339
BSU22610 tyrA prephenate dehydrogenase (RefSeq) 107, 187
BSU22620 hisC histidinol-phosphate aminotransferase (RefSeq) 4, 107
BSU22630 trpA tryptophan synthase subunit alpha (RefSeq) 4, 107
BSU22640 trpB tryptophan synthase subunit beta (RefSeq) 4, 107
BSU22650 trpF N-(5'-phosphoribosyl)anthranilate isomerase (RefSeq) 4, 107
BSU22660 trpC indole-3-glycerol-phosphate synthase (RefSeq) 4, 107
BSU22670 trpD anthranilate phosphoribosyltransferase (RefSeq) 4, 107
BSU22680 trpE anthranilate synthase component I (RefSeq) 4, 107
BSU22690 aroH chorismate mutase (RefSeq) 107, 343
BSU22700 aroB 3-dehydroquinate synthase (RefSeq) 107, 343
BSU22710 aroF chorismate synthase (RefSeq) 107, 343
BSU22780 folE GTP cyclohydrolase I (RefSeq) 228, 266
BSU23370 ypuA hypothetical protein (RefSeq) 7, 266
BSU25160 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (RefSeq) 226, 266
BSU25400 yqeY hypothetical protein (RefSeq) 7, 266
BSU25410 rpsU 30S ribosomal protein S21 (RefSeq) 7, 266
BSU27580 yrvJ putative N-acetylmuramoyl-L-alanine amidase, family 3 (RefSeq) 266, 322
BSU27990 minD ATPase activator of MinC (RefSeq) 212, 266
BSU28040 radC DNA repair protein RadC (RefSeq) 98, 266
BSU28050 maf Maf-like protein (RefSeq) 98, 266
BSU28470 lysC aspartate kinase (RefSeq) 266, 300
BSU30740 mntD manganese ABC transporter (permease) (RefSeq) 4, 107
BSU30750 mntC manganese ABC transporter (permease) (RefSeq) 4, 107
BSU30760 mntB manganese ABC transporter (ATP-binding protein) (RefSeq) 4, 107
BSU30770 mntA manganese ABC transporter (manganese binding lipoprotein) (RefSeq) 4, 107
BSU33480 bdbD thiol-disulfide oxidoreductase (RefSeq) 4, 107
BSU33870 yvbI putative permease (RefSeq) 197, 266
BSU35760 tagB teichoic acid primase, CDP-glycerol:N-acetyl-beta-d-mannosaminyl-1, 4-N-acetyl-d-glucosaminyldiphosphoundecaprenyl glycerophosphotransferase (RefSeq) 226, 266
BSU37160 rpoE DNA-directed RNA polymerase subunit delta (RefSeq) 197, 266
BSU38140 qoxD cytochrome aa3-600 quinol oxidase (subunit IV) (RefSeq) 107, 343
BSU38150 qoxC cytochrome aa3-600 quinol oxidase (subunit III) (RefSeq) 107, 343
BSU38160 qoxB cytochrome aa3-600 quinol oxidase (subunit I) (RefSeq) 107, 343
BSU38170 qoxA cytochrome aa3-600 quinol oxidase (subunit II) (RefSeq) 107, 343
BSU40920 yyaF GTP-dependent nucleic acid-binding protein EngD (RefSeq) 98, 266
BSU41060 rpmH 50S ribosomal protein L34 (RefSeq) 119, 266
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 BSU16960
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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