Organism : Bacillus subtilis | Module List :
BSU15640 yloA

putative persistent RNA/DNA binding protein (RefSeq)

CircVis
Functional Annotations (1)
Function System
Predicted RNA-binding protein homologous to eukaryotic snRNP cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU15640
(Mouseover regulator name to see its description)

BSU15640 is regulated by 19 influences and regulates 15 modules.
Regulators for BSU15640 yloA (19)
Regulator Module Operator
BSU04680 78 tf
BSU05330 78 tf
BSU15640 78 tf
BSU17450 78 tf
BSU19120 78 tf
BSU27320 78 tf
BSU28820 78 tf
BSU31530 78 tf
BSU33080 78 tf
BSU37650 78 tf
BSU04680 398 tf
BSU15640 398 tf
BSU19120 398 tf
BSU24770 398 tf
BSU27320 398 tf
BSU28820 398 tf
BSU31530 398 tf
BSU36020 398 tf
BSU37650 398 tf

Warning: BSU15640 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
5110 1.60e-03 AAaAaAGG
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5111 1.30e+03 AaAAGGAgTgaAtag
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5706 9.10e-04 atAaAaaAGgAgGgA
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5707 2.60e-01 ttaTaaTtATAatGg.A.AgccaA
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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 BSU15640

BSU15640 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted RNA-binding protein homologous to eukaryotic snRNP cog/ cog
Module neighborhood information for BSU15640

BSU15640 has total of 36 gene neighbors in modules 78, 398
Gene neighbors (36)
Gene Common Name Description Module membership
BSU10030 hinT Hit-family hydrolase (RefSeq) 78, 398
BSU11160 yitW hypothetical protein (RefSeq) 398, 412
BSU13200 rsbRB component of the piezosome (stressosome) (RefSeq) 78, 145
BSU14650 yktB hypothetical protein (RefSeq) 78, 398
BSU14670 suhB inositol monophosphatase (RefSeq) 78, 398
BSU14680 ykzC hypothetical protein (RefSeq) 78, 398
BSU15120 yllA putative nucleoid associated protein (RefSeq) 78, 113
BSU15640 yloA putative persistent RNA/DNA binding protein (RefSeq) 78, 398
BSU16670 ribC bifunctional riboflavin kinase/FMN adenylyltransferase (RefSeq) 78, 324
BSU17280 ymaD putative peroxiredoxin-related protein (RefSeq) 78, 398
BSU18040 yneP putative acyl-CoA thioesterase (RefSeq) 324, 398
BSU18490 rtp replication terminator protein (RefSeq) 78, 381
BSU18500 fabG 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq) 78, 398
BSU19120 czrA transcriptional regulator (multiple metal-sensing ArsR-SmtB transcriptional repressors family) (RefSeq) 78, 291
BSU23620 yqkF NADPH-dependent aldo-keto reductase (RefSeq) 113, 398
BSU23850 zwf glucose-6-phosphate 1-dehydrogenase (RefSeq) 63, 78
BSU23860 yqjI 6-phosphogluconate dehydrogenase (RefSeq) 78, 194
BSU23990 yqiW hypothetical protein (RefSeq) 31, 78
BSU24790 yqgX putative metal-binding hydrolase (RefSeq) 78, 398
BSU25020 sodA superoxide dismutase (RefSeq) 78, 398
BSU27320 greA transcription elongation factor GreA (RefSeq) 63, 78
BSU28220 clpX ATP-dependent protease ATP-binding subunit ClpX (RefSeq) 78, 324
BSU29480 ytxK putative nucleic acid methyltransferase (RefSeq) 78, 398
BSU29490 tpx thiol peroxidase (RefSeq) 78, 398
BSU29820 ytpR putative protein with RNA binding domain (RefSeq) 193, 398
BSU29830 ytpQ hypothetical protein (RefSeq) 193, 398
BSU29840 ytpP putative thiol-disulfide oxidoreductase with thiredoxin domain (RefSeq) 193, 398
BSU29850 ytoQ putative enzyme with sugar binding fold (RefSeq) 68, 398
BSU29860 ytoP glutamyl aminopeptidase (RefSeq) 78, 398
BSU29870 ytzB hypothetical protein (RefSeq) 398, 412
BSU30500 ytpB hypothetical protein (RefSeq) 163, 398
BSU30510 ytpA phospholipase component of bacilysocin synthesis or export (RefSeq) 68, 398
BSU32790 yusG hypothetical protein (RefSeq) 77, 78
BSU32800 yusH glycine cleavage system protein H (RefSeq) 78, 247
BSU34790 trxB thioredoxin reductase (RefSeq) 259, 398
BSU38370 ywbC putative lyase (RefSeq) 77, 78
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 BSU15640
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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