Organism : Bacillus subtilis | Module List :
BSU31070 yuaC

putative transcriptional regulator (RefSeq)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU31070
(Mouseover regulator name to see its description)

BSU31070 is regulated by 22 influences and regulates 6 modules.
Regulators for BSU31070 yuaC (22)
Regulator Module Operator
BSU00800 293 tf
BSU04460 293 tf
BSU10150 293 tf
BSU13880 293 tf
BSU24250 293 tf
BSU31410 293 tf
BSU34170 293 tf
BSU37580 293 tf
BSU40410 293 tf
BSU02680 409 tf
BSU05330 409 tf
BSU09830 409 tf
BSU10150 409 tf
BSU13210 409 tf
BSU13880 409 tf
BSU18420 409 tf
BSU26670 409 tf
BSU26720 409 tf
BSU27520 409 tf
BSU31070 409 tf
BSU36110 409 tf
BSU38310 409 tf

Warning: BSU31070 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
5524 5.40e+00 gtAAaA.AAAA
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5525 1.40e+01 AaAatGgGaaTttgACaG
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5724 2.10e-05 ggGgagaaaTcAataaaAAaaAtc
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5725 9.00e-04 cATAtGGTttct.tAtaGtcAAag
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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 BSU31070

BSU31070 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for BSU31070

BSU31070 has total of 48 gene neighbors in modules 293, 409
Gene neighbors (48)
Gene Common Name Description Module membership
BSU00570 yabM putative exporter (RefSeq) 66, 409
BSU02500 ycbG transcriptional regulator (GntR family) (RefSeq) 233, 293
BSU02860 adcC Zn(II) transporter (ATP-binding protein) (RefSeq) 271, 409
BSU02870 adcB high affinity Zn(II) ABC transporter (permease) (RefSeq) 271, 409
BSU04570 murF UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanine ligase (RefSeq) 170, 409
BSU06120 ydjB hypothetical protein (RefSeq) 150, 409
BSU06600 pcrB geranylgeranylglyceryl phosphate synthase-like protein (RefSeq) 293, 314
BSU07710 yflE putative exported enzyme and anion transporter (RefSeq) 14, 409
BSU07980 pdaA exported N-acetylmuramic acid deacetylase (RefSeq) 66, 293
BSU08540 yfhI putative efflux transporter (RefSeq) 67, 293
BSU08940 yhbD putative nucleic acid binding protein (RefSeq) 50, 293
BSU08950 yhbE hypothetical protein (RefSeq) 50, 293
BSU10110 pbpF penicillin-binding protein 2C required for spore germination (RefSeq) 293, 370
BSU13100 ykkD efflux transporter (RefSeq) 66, 293
BSU13730 queD 6-pyruvoyl tetrahydrobiopterin synthase-like; queuosine biosynthesis (RefSeq) 319, 409
BSU13740 queE queuosine biosynthesis enzyme (RefSeq) 319, 409
BSU13750 ykvM 7-cyano-7-deazaguanine reductase (RefSeq) 23, 409
BSU16120 topA DNA topoisomerase I (RefSeq) 292, 409
BSU22340 nth endonuclease III (RefSeq) 67, 293
BSU22350 dnaD DNA-remodelling primosomal protein (RefSeq) 67, 293
BSU23560 mleN malate-H+/Na+-lactate antiporter (RefSeq) 228, 293
BSU23570 aspA aspartate ammonia-lyase (RefSeq) 258, 293
BSU23580 ansA exported L-asparaginase (RefSeq) 258, 293
BSU23800 proI pyrroline-5-carboxylate reductase (RefSeq) 66, 409
BSU25170 yqfO hypothetical protein (RefSeq) 202, 293
BSU25510 lepA GTP-binding protein LepA (RefSeq) 204, 409
BSU26580 bltR transcriptional regulator (RefSeq) 115, 409
BSU26590 blt efflux transporter (RefSeq) 115, 409
BSU27600 relA GTP pyrophosphokinase (RelA/SpoT) (RefSeq) 225, 293
BSU28990 dnaB helicase loading protein; replication initiation membrane attachment protein (RefSeq) 228, 293
BSU29200 accA acetyl-CoA carboxylase carboxyltransferase subunit alpha (RefSeq) 241, 293
BSU29210 accD acetyl-CoA carboxylase subunit beta (RefSeq) 241, 293
BSU30035 BSU30035 None 235, 409
BSU31050 gbsB choline dehydrogenase (RefSeq) 293, 409
BSU31060 gbsA glycine betaine aldehyde dehydrogenase, NAD+-dependent (RefSeq) 293, 409
BSU31070 yuaC putative transcriptional regulator (RefSeq) 293, 409
BSU31410 yugG putative transcriptional regulator (Lrp/AsnC family) (RefSeq) 67, 293
BSU34170 ganR transcriptional regulator (LacI family) (RefSeq) 167, 293
BSU35210 yvkA putative efflux transporter (RefSeq) 38, 409
BSU35730 tagE UDP-glucose:polyglycerol phosphate alpha-glucosyltransferase (RefSeq) 212, 409
BSU36120 ywrB putative anion transporter (RefSeq) 233, 409
BSU36130 ywrA putative anion transporter (RefSeq) 327, 409
BSU38120 rodA factor involved in extension of the lateral walls of the cell (RefSeq) 38, 409
BSU38310 ywbI putative transcriptional regulator (LysR family) (RefSeq) 291, 409
BSU38320 ywbH holin-like protein (RefSeq) 132, 409
BSU38330 lrgB anti-holin factor controlling activity of murein hydrolases (RefSeq) 291, 409
BSU38840 yxkD efflux transporter (RefSeq) 37, 293
VIMSS39424 VIMSS39424 None 293, 325
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 BSU31070
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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