Organism : Bacillus subtilis | Module List :
BSU19560 yodD

putative hydrolase (RefSeq)

CircVis
Functional Annotations (2)
Function System
Predicted esterase cog/ cog
carboxylesterase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU19560
(Mouseover regulator name to see its description)

BSU19560 is regulated by 35 influences and regulates 0 modules.
Regulators for BSU19560 yodD (35)
Regulator Module Operator
BSU00560 50 tf
BSU01640 50 tf
BSU01730 50 tf
BSU03170 50 tf
BSU05370 50 tf
BSU09060 50 tf
BSU09830 50 tf
BSU10830 50 tf
BSU10840 50 tf
BSU14730 50 tf
BSU23100 50 tf
BSU27000 50 tf
BSU27170 50 tf
BSU33670 50 tf
BSU35050 50 tf
BSU38310 50 tf
BSU40010 50 tf
BSU40050 50 tf
BSU00830 111 tf
BSU01730 111 tf
BSU05370 111 tf
BSU05580 111 tf
BSU05850 111 tf
BSU09430 111 tf
BSU13150 111 tf
BSU15690 111 tf
BSU24320 111 tf
BSU27110 111 tf
BSU33230 111 tf
BSU33580 111 tf
BSU36110 111 tf
BSU36160 111 tf
BSU37550 111 tf
BSU38420 111 tf
BSU40540 111 tf

Warning: BSU19560 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
5058 7.80e-01 aaTATcagGAAAtcGAGaTa
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5059 4.70e+02 CgTGTCtAacCCCTTTcgT
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5176 6.30e+01 tttttaAA.aGAggaaaa.aG
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5177 3.10e+02 A.A.agaAag..Ggc
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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 BSU19560

BSU19560 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted esterase cog/ cog
carboxylesterase activity go/ molecular_function
Module neighborhood information for BSU19560

BSU19560 has total of 49 gene neighbors in modules 50, 111
Gene neighbors (49)
Gene Common Name Description Module membership
BSU00180 tadA tRNA specific adenosine deaminase (RefSeq) 111, 123
BSU04300 ydaM putative glycosyltransferase associated to biofilm formation (RefSeq) 50, 317
BSU04750 ydcF hypothetical protein (RefSeq) 50, 137
BSU05580 ydgC putative transcriptional regulator (RefSeq) 111, 262
BSU05590 ydgD hypothetical protein (RefSeq) 111, 262
BSU05600 ydgE putative N-acetyltransferase (RefSeq) 111, 216
BSU05610 vmlR ATP-binding cassette efflux transporter (RefSeq) 111, 354
BSU07735 BSU07735 None 111, 262
BSU08940 yhbD putative nucleic acid binding protein (RefSeq) 50, 293
BSU08950 yhbE hypothetical protein (RefSeq) 50, 293
BSU10640 sbcD DNA repair exonuclease (RefSeq) 50, 361
BSU10650 sbcC DNA ATP-dependent repair enzyme (RefSeq) 50, 361
BSU10660 yisB putative nuclease component (RefSeq) 50, 361
BSU10820 yisQ putative Na+driven efflux transporter (RefSeq) 50, 164
BSU10830 yisR putative transcriptional regulator (AraC/XylS family) (RefSeq) 50, 164
BSU10840 degA transcriptional regulator (LacI family) (RefSeq) 50, 164
BSU10890 yisX hypothetical protein (RefSeq) 111, 262
BSU12870 mhqA putative hydroquinone-specific extradiol dioxygenase (RefSeq) 50, 412
BSU13150 ohrR transcriptional regulator sensing organic peroxides (RefSeq) 111, 123
BSU13850 zosA Zn transporter (RefSeq) 111, 249
BSU14400 fruA phosphotransferase system (PTS) fructose-specific enzyme IIABC component (RefSeq) 50, 164
BSU15060 ylbM hypothetical protein (RefSeq) 111, 123
BSU15230 murB UDP-N-acetylenolpyruvoylglucosamine reductase (RefSeq) 1, 50
BSU19560 yodD putative hydrolase (RefSeq) 50, 111
BSU19570 yodE putative lyase/dioxygenase (RefSeq) 50, 111
BSU21870 ilvD dihydroxy-acid dehydratase (RefSeq) 28, 111
BSU23550 mleA NAD-dependent malic enzyme (conversion of malate into pyruvate) (RefSeq) 50, 228
BSU23640 yqkD putative hydrolase (RefSeq) 111, 373
BSU23790 yqjP putative metal-dependent hydrolase (RefSeq) 37, 50
BSU27160 cypB cytochrome P450 CYP102A3 (RefSeq) 50, 240
BSU27170 bscR transcriptional regulator for cypB (RefSeq) 50, 240
BSU32180 yutK putative Na+(H+)/nucleoside cotransporter (RefSeq) 50, 67
BSU32660 yurT putative methylglyoxalase (RefSeq) 50, 233
BSU32770 yusE putative thiol-disulfide oxidoreductase with thioredoxin domain (RefSeq) 111, 354
BSU33230 sigO alternative sigma factor (RefSeq) 111, 341
BSU33500 copA copper transporter ATPase (RefSeq) 37, 50
BSU33510 copZ copper insertion chaperone and transporter component (RefSeq) 37, 50
BSU33560 yvaD putative integral inner membrane protein (RefSeq) 111, 318
BSU33570 yvaE putative metabolite-efflux transporter (RefSeq) 111, 318
BSU33580 yvaF putative transcriptional regulator (RefSeq) 111, 318
BSU36480 ywoD putative efflux transporter (RefSeq) 50, 307
BSU36490 ywoC putative hydrolase (RefSeq) 50, 307
BSU37540 ywhB 4-oxalocrotonate tautomerase (RefSeq) 111, 115
BSU37550 ywhA putative transcriptional regulator (MarR family) (RefSeq) 111, 123
BSU37570 mmr toxic compound efflux transporter (RefSeq) 37, 50
BSU37960 ywdH putative aldehyde dehydrogenase (RefSeq) 111, 243
BSU37970 ung uracil-DNA glycosylase (RefSeq) 1, 50
BSU37990 ywdE putative integral inner membrane protein (RefSeq) 38, 111
BSU38000 ywdD putative integral inner membrane protein (RefSeq) 38, 111
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 BSU19560
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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