Organism : Bacillus subtilis | Module List :
BSU08510 yfhF

putative nucleotide binding protein (RefSeq)

CircVis
Functional Annotations (5)
Function System
Predicted nucleoside-diphosphate sugar epimerase cog/ cog
catalytic activity go/ molecular_function
cellular metabolic process go/ biological_process
coenzyme binding go/ molecular_function
yfcH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU08510
(Mouseover regulator name to see its description)

BSU08510 is regulated by 8 influences and regulates 0 modules.
Regulators for BSU08510 yfhF (8)
Regulator Module Operator
BSU04730 352 tf
BSU09690 352 tf
BSU24770 352 tf
BSU04650 236 tf
BSU04730 236 tf
BSU09690 236 tf
BSU15880 236 tf
BSU24770 236 tf

Warning: BSU08510 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
5414 9.70e-05 GaaAAagGaGaT
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5415 3.20e-01 ttt.tcTatTcttTaatTgC
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5628 1.40e+01 gtttactttTTagaaAAA..g
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5629 7.80e+01 aAagGGAG
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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 BSU08510

BSU08510 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted nucleoside-diphosphate sugar epimerase cog/ cog
catalytic activity go/ molecular_function
cellular metabolic process go/ biological_process
coenzyme binding go/ molecular_function
yfcH tigr/ tigrfam
Module neighborhood information for BSU08510

BSU08510 has total of 28 gene neighbors in modules 236, 352
Gene neighbors (28)
Gene Common Name Description Module membership
BSU00160 yaaH spore peptidoglycan hydrolase (RefSeq) 236, 403
BSU00170 yaaI putative isochorismatase (RefSeq) 236, 403
BSU04720 rsbW serine-protein kinase RsbW (RefSeq) 320, 352
BSU04730 sigB RNA polymerase sigma factor SigB (RefSeq) 320, 352
BSU04740 rsbX serine phosphatase (RefSeq) 320, 352
BSU07750 yflA putative aminoacid transporter (RefSeq) 352, 403
BSU07880 yfkJ protein-tyrosine-phosphatase (RefSeq) 149, 352
BSU07900 yfkH putative integral inner membrane protein with ribonuclease fold (RefSeq) 352, 391
BSU07920 yfkE putative H+/Ca2+ antiporter (RefSeq) 59, 352
BSU07930 yfkD hypothetical protein (RefSeq) 59, 352
BSU08510 yfhF putative nucleotide binding protein (RefSeq) 236, 352
BSU08570 yfhK hypothetical protein (RefSeq) 236, 352
BSU08580 yfhL SdpC immunity factor (RefSeq) 236, 391
BSU08590 yfhM putative hydrolase (RefSeq) 137, 236
BSU13020 ykgA putative aminohydrolase (RefSeq) 320, 352
BSU14660 ykzI hypothetical protein (RefSeq) 236, 352
BSU18510 yoxC hypothetical protein (RefSeq) 236, 403
BSU24000 bmrU putative diacylglycerol kinase (RefSeq) 236, 352
BSU24740 yqxL putative CorA-type Mg(2+) transporter (RefSeq) 236, 403
BSU24750 yqhB putative membrane associated protein (RefSeq) 236, 403
BSU24760 rsbRD component of the piezosome (stressosome) (RefSeq) 352, 391
BSU31280 yugU hypothetical protein (RefSeq) 236, 403
BSU35830 ywtG putative carbohydrate transporter (RefSeq) 137, 352
BSU37240 ywiE cardiolipin synthetase (RefSeq) 352, 391
BSU38180 ywzA hypothetical protein (RefSeq) 203, 236
BSU38430 gspA putative glycosyl transferase (general stress protein) (RefSeq) 203, 352
BSU39810 csbC putative sugar transporter (RefSeq) 59, 352
BSU39840 yxbG short chain dehydrogenase (RefSeq) 236, 403
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 BSU08510
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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