Organism : Bacillus subtilis | Module List :
BSU04020 yczH

putative hydrolase (RefSeq)

CircVis
Functional Annotations (2)
Function System
Dienelactone hydrolase and related enzymes cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU04020
(Mouseover regulator name to see its description)

BSU04020 is regulated by 10 influences and regulates 0 modules.
Regulators for BSU04020 yczH (10)
Regulator Module Operator
BSU00980 145 tf
BSU15640 145 tf
BSU23090 145 tf
BSU23100 145 tf
BSU27320 145 tf
BSU28820 145 tf
BSU35650 145 tf
BSU38220 145 tf
BSU05850 64 tf
BSU09650 64 tf

Warning: BSU04020 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
5084 4.70e-02 aaaaAggggaG
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5085 1.20e+02 TaTATTTTaccATtAaActGTgAC
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5240 1.10e+01 TAtaATataAaaa..acaaaa
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5241 1.90e+03 aAGcGGtTtTg
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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 BSU04020

BSU04020 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Dienelactone hydrolase and related enzymes cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for BSU04020

BSU04020 has total of 61 gene neighbors in modules 64, 145
Gene neighbors (61)
Gene Common Name Description Module membership
BSU00980 sigH RNA polymerase factor sigma-70 (RefSeq) 36, 145
BSU00990 rpmG 50S ribosomal protein L33 (RefSeq) 64, 200
BSU03450 hxlB 6-phospho-3-hexuloisomerase (PHI) (RefSeq) 64, 296
BSU03460 hxlA 3-hexulose-6-phosphate synthase (HPS) (RefSeq) 64, 296
BSU04020 yczH putative hydrolase (RefSeq) 64, 145
BSU04030 ycsD putative hydroxymyristoyl-(acyl carrier protein) dehydratase (RefSeq) 145, 177
BSU04120 yczI hypothetical protein (RefSeq) 145, 263
BSU08390 yfiT metal-dependent hydrolase (RefSeq) 145, 152
BSU09490 yhdJ putative acetyltransferase (RefSeq) 145, 318
BSU09540 plsC 1-acylglycerol-phosphate (1-acyl-G3P) acyltransferase (RefSeq) 64, 404
BSU09600 crcBA camphor resistance protein CrcB (RefSeq) 64, 115
BSU10010 trpP tryptophan transporter (RefSeq) 64, 94
BSU10880 yisV putative PLP-dependent transcriptional regulator (RefSeq) 64, 318
BSU10990 yitH putative N-acetyltransferase (RefSeq) 64, 171
BSU11000 yitI putative N-acetyltransferase (RefSeq) 64, 219
BSU11270 yjzD hypothetical protein (RefSeq) 64, 157
BSU11280 yjaU hypothetical protein (RefSeq) 64, 157
BSU11480 yjbB putative exporter (RefSeq) 64, 350
BSU11510 yjbE putative transporter component (RefSeq) 64, 115
BSU11910 yjcM hypothetical protein (RefSeq) 7, 145
BSU12500 xkdA PBSX phage protein, putative peptidase (RefSeq) 64, 96
BSU13070 ykkA hypothetical protein (RefSeq) 64, 171
BSU13080 ykkB putative N-acetyltransferase (RefSeq) 64, 171
BSU13200 rsbRB component of the piezosome (stressosome) (RefSeq) 78, 145
BSU14540 ykzG hypothetical protein (RefSeq) 36, 145
BSU14570 ykyA putative chromosome partitioning protein (RefSeq) 36, 145
BSU14760 ylaF hypothetical protein (RefSeq) 36, 145
BSU15280 ftsA cell-division protein essential fo Z-ring assembly (RefSeq) 63, 145
BSU15290 ftsZ cell division protein FtsZ (RefSeq) 63, 145
BSU15420 divIVA cell-division initiation protein (RefSeq) 64, 402
BSU18620 yoaI putative 4-hydroxyphenylacetate-3-hydroxylase (RefSeq) 64, 379
BSU18690 yoaP hypothetical protein (RefSeq) 64, 129
BSU19090 yobU putative effector of transcriptional regulator (RefSeq) 64, 239
BSU19100 yobV putative transcriptional regulator (RefSeq) 64, 170
BSU21830 ypjQ putative phosphatidylglycerophosphatase (RefSeq) 64, 404
BSU23090 rsiX negative regulator of sigma(X) activity (RefSeq) 145, 159
BSU23100 sigX RNA polymerase sigma factor SigX (RefSeq) 145, 159
BSU23220 scpA segregation and condensation protein A (RefSeq) 145, 166
BSU25050 yqgA hypothetical protein (RefSeq) 7, 145
BSU26160 yqbC conserved hypothetical protein; skin element (RefSeq) 145, 291
BSU26230 yqaP conserved hypothetical protein; skin element (RefSeq) 25, 64
BSU26240 yqaO conserved hypothetical protein; skin element (RefSeq) 64, 216
BSU27800 yrzH hypothetical protein (RefSeq) 64, 258
BSU27810 yrbD sodium/proton-dependent alanine transporter (RefSeq) 64, 304
BSU30670 luxS S-ribosylhomocysteinase (RefSeq) 49, 64
BSU30680 ytjA hypothetical protein (RefSeq) 64, 115
BSU31460 kapB factor required for KinB signal transduction and activation of the phosphorelay to sporulation (RefSeq) 145, 150
BSU31580 maeN Na+/malate symporter (RefSeq) 64, 238
BSU31710 comQ isoprenyl transferase (pre-ComX modification) (RefSeq) 145, 317
BSU33040 fumC fumarate hydratase (RefSeq) 70, 145
BSU33890 yvbK putative acyltransferase (RefSeq) 36, 145
BSU35440 yvyF putative regulator of flagella formation (RefSeq) 7, 145
BSU35480 yviA hypothetical protein (RefSeq) 145, 155
BSU35650 lytR membrane-bound transcriptional regulator LytR (RefSeq) 145, 166
BSU35880 pgsA capsular polyglutamate synthetase (RefSeq) 64, 318
BSU36320 ywpG hypothetical protein (RefSeq) 64, 318
BSU38550 ywaA branched-chain amino acid aminotransferase (RefSeq) 123, 145
BSU38860 galE UDP-glucose 4-epimerase (RefSeq) 36, 145
BSU40200 yydD hypothetical protein (RefSeq) 36, 145
BSU40210 yydC hypothetical protein (RefSeq) 36, 145
BSU40220 yydB putative phosphohydrolase (RefSeq) 36, 145
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 BSU04020
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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