Organism : Bacillus subtilis | Module List :
VIMSS37404

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VIMSS37404
(Mouseover regulator name to see its description)

VIMSS37404 is regulated by 24 influences and regulates 0 modules.
Regulators for VIMSS37404 (24)
Regulator Module Operator
BSU00830 70 tf
BSU05700 70 tf
BSU08300 70 tf
BSU10560 70 tf
BSU13450 70 tf
BSU19120 70 tf
BSU24020 70 tf
BSU31530 70 tf
BSU33010 70 tf
BSU35050 70 tf
BSU35650 70 tf
BSU36020 70 tf
BSU37650 70 tf
BSU38070 70 tf
BSU01010 287 tf
BSU01640 287 tf
BSU01810 287 tf
BSU02680 287 tf
BSU09330 287 tf
BSU10860 287 tf
BSU16600 287 tf
BSU24320 287 tf
BSU37160 287 tf
BSU38600 287 tf

Warning: VIMSS37404 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
5096 1.50e-01 gg.aAaa.aAG.aaAatcT.c
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5097 2.70e+02 ggaGGGG
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5512 4.90e-05 AAGGaGaG
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5513 2.20e+02 CATAaa.TagaaaGagGTgTta
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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 VIMSS37404

Warning: No Functional annotations were found!

Module neighborhood information for VIMSS37404

VIMSS37404 has total of 47 gene neighbors in modules 70, 287
Gene neighbors (47)
Gene Common Name Description Module membership
BSU00620 divIC cell-division initiation protein (RefSeq) 70, 324
BSU00900 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (RefSeq) 70, 388
BSU00910 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (RefSeq) 70, 113
BSU02090 ybxI exported beta-lactamase (RefSeq) 171, 287
BSU05220 ydeJ putative lipoprotein (RefSeq) 171, 287
BSU07440 yfmK putative acetyltransferase (RefSeq) 171, 287
BSU09860 khtT K+/H+ antiporter for K+ efflux (RefSeq) 31, 70
BSU09870 khtS K+/H+ antiporter for K+ efflux (RefSeq) 31, 70
BSU10300 aprE serine alkaline protease (subtilisin E) (RefSeq) 114, 287
BSU11140 yitU putative phosphatase (RefSeq) 70, 254
BSU13640 spo0E negative regulatory phosphatase acting on Spo0A-P (sporulation) (RefSeq) 70, 91
BSU13940 ykwB putative acetyltransferase (RefSeq) 171, 287
BSU13980 pbpH penicillin-binding enzyme for formation of rod-shaped peptidoglycan cell wall (RefSeq) 70, 94
BSU14820 ylaL hypothetical protein (RefSeq) 70, 296
BSU15100 ylbP hypothetical protein (RefSeq) 70, 381
BSU17500 ynaB hypothetical protein (RefSeq) 70, 91
BSU18350 dacC D-alanyl-D-alanine carboxypeptidase (RefSeq) 136, 287
BSU18360 yoxA putative epimerase (RefSeq) 136, 287
BSU18370 yoeA putative efflux transporter (RefSeq) 171, 287
BSU18380 iseA inhibitor of cell-separation enzymes (RefSeq) 70, 381
BSU18890 yobF hypothetical protein (RefSeq) 70, 310
BSU24780 yqgY hypothetical protein (RefSeq) 70, 171
BSU24810 yqgV hypothetical protein (RefSeq) 70, 166
BSU26370 yqaC hypothetical protein (RefSeq) 171, 287
BSU26470 yrkL putative NAD(P)H oxidoreductase (RefSeq) 70, 310
BSU27380 yrzB hypothetical protein (RefSeq) 70, 166
BSU27390 yrrK Holliday junction resolvase-like protein (RefSeq) 70, 310
BSU27400 yrzL hypothetical protein (RefSeq) 70, 310
BSU28420 ysmA hypothetical protein (RefSeq) 171, 287
BSU30360 yttA hypothetical protein (RefSeq) 171, 287
BSU31945 BSU31945 None 69, 287
BSU33040 fumC fumarate hydratase (RefSeq) 70, 145
BSU34540 clpP ATP-dependent Clp protease proteolytic subunit (RefSeq) 68, 70
BSU36330 ywpF hypothetical protein (RefSeq) 70, 310
BSU37130 spo0F two-component response regulator (RefSeq) 70, 113
BSU38470 ywaD double-zinc aminopeptidase (RefSeq) 101, 287
BSU40022 BSU40022 None 117, 287
BSU40230 yydA rRNA large subunit methyltransferase (RefSeq) 36, 70
BSU40250 yycR putative dehydrogenase (RefSeq) 136, 287
BSU40290 yycN putative N-acetyltransferase (RefSeq) 114, 287
BSU40300 rapG response regulator aspartate phosphatase (RefSeq) 101, 287
BSU40630 yybI inner spore coat protein (RefSeq) 114, 287
BSU40640 yybH hypothetical protein (RefSeq) 171, 287
VIMSS37404 VIMSS37404 None 70, 287
VIMSS38706 VIMSS38706 None 117, 287
VIMSS39865 VIMSS39865 None 158, 287
VIMSS40339 VIMSS40339 None 70, 287
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 VIMSS37404
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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