Organism : Bacillus subtilis | Module List :
BSU35310 yvyD

ribosome-associated sigma 54 modulation protein (RefSeq)

CircVis
Functional Annotations (2)
Function System
Ribosome-associated protein Y (PSrp-1) cog/ cog
yfiA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU35310
(Mouseover regulator name to see its description)

BSU35310 is regulated by 27 influences and regulates 0 modules.
Regulators for BSU35310 yvyD (27)
Regulator Module Operator
BSU05270 381 tf
BSU09430 381 tf
BSU09990 381 tf
BSU10510 381 tf
BSU10860 381 tf
BSU13760 381 tf
BSU19120 381 tf
BSU20820 381 tf
BSU30020 381 tf
BSU33080 381 tf
BSU36020 381 tf
BSU37650 381 tf
BSU38070 381 tf
BSU38600 381 tf
BSU01010 296 tf
BSU02680 296 tf
BSU04680 296 tf
BSU04730 296 tf
BSU09690 296 tf
BSU09990 296 tf
BSU21020 296 tf
BSU24770 296 tf
BSU33080 296 tf
BSU33740 296 tf
BSU36020 296 tf
BSU37650 296 tf
BSU38600 296 tf

Warning: BSU35310 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
5530 4.30e-05 CtCctTTTtc
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5531 6.30e-01 GGAGGtat
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5674 9.40e-01 ta.AAaGgagG
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5675 4.00e+04 GCGGCC
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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 BSU35310

BSU35310 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Ribosome-associated protein Y (PSrp-1) cog/ cog
yfiA tigr/ tigrfam
Module neighborhood information for BSU35310

BSU35310 has total of 45 gene neighbors in modules 296, 381
Gene neighbors (45)
Gene Common Name Description Module membership
BSU01540 salA Mrp family regulator (RefSeq) 113, 296
BSU03450 hxlB 6-phospho-3-hexuloisomerase (PHI) (RefSeq) 64, 296
BSU03460 hxlA 3-hexulose-6-phosphate synthase (HPS) (RefSeq) 64, 296
BSU03470 hxlR positive regulator of hxlAB expression (RefSeq) 91, 296
BSU05260 ydeN alpha/beta hydrolase (RefSeq) 373, 381
BSU05270 ydzF putative transcriptional regulator (RefSeq) 109, 381
BSU05400 ydfG hypothetical protein (RefSeq) 373, 381
BSU05760 ydhH hypothetical protein (RefSeq) 373, 381
BSU05770 ydhI putative acetyltransferase (RefSeq) 373, 381
BSU08210 malQ maltose and maltodextrin ABC transporter subunit (ATP-binding protein) (RefSeq) 123, 296
BSU08220 yfiC putative ABC transporter (ATP-binding protein) (RefSeq) 113, 296
BSU09690 nhaX stress response protein, UspA family (RefSeq) 137, 296
BSU09980 yhaI hypothetical protein (RefSeq) 373, 381
BSU10040 ecsA ABC transporter (ATP-binding protein) (RefSeq) 31, 381
BSU10070 yhaA putative amidohydrolase (RefSeq) 101, 381
BSU10200 yhfE putative endoglucanase (RefSeq) 101, 296
BSU10410 yhzC hypothetical protein (RefSeq) 249, 381
BSU11840 yjcF putative acetyltransferase (RefSeq) 101, 296
BSU11850 yjcG hypothetical protein (RefSeq) 101, 296
BSU11860 yjcH putative hydrolase (RefSeq) 101, 296
BSU13540 ogt O6-alkylguanine DNA alkyltransferase (RefSeq) 373, 381
BSU14820 ylaL hypothetical protein (RefSeq) 70, 296
BSU15100 ylbP hypothetical protein (RefSeq) 70, 381
BSU18380 iseA inhibitor of cell-separation enzymes (RefSeq) 70, 381
BSU18490 rtp replication terminator protein (RefSeq) 78, 381
BSU19150 yocB hypothetical protein (RefSeq) 203, 296
BSU19680 yozE hypothetical protein (RefSeq) 373, 381
BSU29410 ytkL metal-dependent hydrolase (RefSeq) 68, 296
BSU29420 fabG 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq) 252, 296
BSU29760 ytxJ hypothetical protein (RefSeq) 296, 320
BSU29770 ytxH hypothetical protein (RefSeq) 296, 320
BSU29780 ytxG hypothetical protein (RefSeq) 296, 320
BSU31030 yuaE hypothetical protein (RefSeq) 373, 381
BSU31910 yukE hypothetical protein (RefSeq) 31, 296
BSU32060 yuiD putative integral inner membrane protein (RefSeq) 354, 381
BSU32160 yutM putative chaperone involved in Fe-S cluster assembly (RefSeq) 109, 381
BSU32990 mrgA metalloregulation DNA-binding stress protein (RefSeq) 296, 359
BSU33850 yvbG putative integral inner membrane protein (RefSeq) 167, 296
BSU35310 yvyD ribosome-associated sigma 54 modulation protein (RefSeq) 296, 381
BSU36580 ywnF hypothetical protein (RefSeq) 381, 412
BSU37670 ywfI putative heme peroxidase (RefSeq) 381, 412
BSU38110 nfrA FMN-containing NADPH-linked nitro/flavin reductase (RefSeq) 381, 412
BSU39250 yxiE phosphate starvation protein (universal stress protein A family) (RefSeq) 249, 381
BSU40040 glxK glycerate kinase (RefSeq) 68, 296
BSU40790 yyaO hypothetical protein (RefSeq) 373, 381
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 BSU35310
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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