Organism : Bacillus subtilis | Module List :
BSU09060 yhcF

putative transcriptional regulator (GntR family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU09060
(Mouseover regulator name to see its description)

BSU09060 is regulated by 28 influences and regulates 6 modules.
Regulators for BSU09060 yhcF (28)
Regulator Module Operator
BSU03080 102 tf
BSU08990 102 tf
BSU09060 102 tf
BSU09330 102 tf
BSU11500 102 tf
BSU18460 102 tf
BSU29740 102 tf
BSU30020 102 tf
BSU30260 102 tf
BSU33080 102 tf
BSU33840 102 tf
BSU36630 102 tf
BSU38220 102 tf
BSU40710 102 tf
BSU03170 11 tf
BSU03850 11 tf
BSU04100 11 tf
BSU09060 11 tf
BSU13210 11 tf
BSU16600 11 tf
BSU19050 11 tf
BSU19070 11 tf
BSU24100 11 tf
BSU33080 11 tf
BSU34200 11 tf
BSU37160 11 tf
BSU38910 11 tf
BSU40670 11 tf

Warning: BSU09060 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
4984 1.30e+01 TgCCttttctcctg
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4985 4.40e+03 TtTaTatggaaaaA
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5158 8.40e+00 C.aCCTTTttc
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5159 2.40e+03 gGAaAggAg
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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 BSU09060

BSU09060 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU09060

BSU09060 has total of 47 gene neighbors in modules 11, 102
Gene neighbors (47)
Gene Common Name Description Module membership
BSU02260 ybfK carboxylesterase NP (RefSeq) 11, 155
BSU02530 rtpA anti-TRAP regulator (RefSeq) 102, 168
BSU02800 ycdC putative hydrolase (RefSeq) 11, 202
BSU03070 mdr multidrug-efflux transporter (RefSeq) 11, 339
BSU03220 ycgO putative proline/ornithine permease (RefSeq) 11, 261
BSU03790 yclM aspartate kinase (RefSeq) 11, 365
BSU03850 ycnC putative transcriptional regulator (TetR/AcrR family) (RefSeq) 11, 13
BSU04110 lipC lysophopholipase (RefSeq) 11, 307
BSU05250 ydeM putative dehydratase (RefSeq) 23, 102
BSU05440 nap carboxylesterase NP (RefSeq) 11, 341
BSU08040 yfjM hypothetical protein (RefSeq) 102, 361
BSU08050 yfjL hypothetical protein (RefSeq) 102, 255
BSU09050 yhcE putative integral inner membrane orphan protein (RefSeq) 11, 339
BSU09060 yhcF putative transcriptional regulator (GntR family) (RefSeq) 11, 102
BSU09070 yhcG putative ABC transporter ATP-binding protein (RefSeq) 11, 339
BSU09440 citA citrate synthase I (RefSeq) 102, 411
BSU14200 ykuS hypothetical protein (RefSeq) 11, 365
BSU19050 yobQ putative transcriptional regulator (AraC/XylS family) (RefSeq) 11, 261
BSU19060 yobR putative acetyltransferase (RefSeq) 11, 261
BSU19070 yobS putative transcriptional regulator (RefSeq) 11, 327
BSU19220 yocI putative ATP-dependent nucleic acid helicase (RefSeq) 102, 334
BSU19480 yojE putative integral inner membrane protein (RefSeq) 102, 255
BSU19590 ctpA carboxy-terminal processing protease (RefSeq) 102, 309
BSU20040 nrdF ribonucleotide-diphosphate reductase subunit beta (NCBI) 66, 102
BSU21770 ilvA threonine dehydratase (RefSeq) 102, 155
BSU22030 ypbR putative GTP-binding protein (RefSeq) 102, 179
BSU22720 cheR methyl-accepting chemotaxis proteins (MCPs) methyltransferase (RefSeq) 102, 334
BSU23670 yqkA hypothetical protein (RefSeq) 11, 79
BSU23690 yqjY putative acetyltransferase (RefSeq) 11, 79
BSU23750 yqjT putative lyase (RefSeq) 102, 334
BSU23840 yqjK ribonuclease Z (RefSeq) 102, 233
BSU24100 bkdR transcriptional regulator (RefSeq) 11, 261
BSU27200 yrhG putative formate/nitrite transporter (RefSeq) 80, 102
BSU31440 patB C-S lyase (RefSeq) 11, 128
BSU31490 pbpD penicillin-binding protein 4 (RefSeq) 102, 402
BSU32630 yurR putative oxidoreductase (RefSeq) 102, 327
BSU33350 yvsG putative membrane hydrolase (RefSeq) 11, 319
BSU34820 bmrA efflux transporter (ATP-binding and permease protein) (RefSeq) 102, 339
BSU35660 mnaA UDP-N-acetylmannosamine 2-epimerase (RefSeq) 102, 402
BSU37330 argS arginyl-tRNA synthetase (RefSeq) 102, 155
BSU37560 thrZ threonyl-tRNA synthetase (RefSeq) 11, 300
BSU38220 ywcC putative transcriptional regulator (RefSeq) 102, 116
BSU38910 yxjL two-component response regulator [YxjM] (RefSeq) 11, 233
BSU39960 yxaI putative integral inner membrane protein (RefSeq) 11, 13
BSU40670 yybE putative transcriptional regulator (LysR family) (RefSeq) 11, 240
BSU40680 yybD putative acetyltransferase (RefSeq) 11, 240
BSU40690 yybC putative integral inner membrane protein (RefSeq) 11, 402
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 BSU09060
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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