Organism : Bacillus subtilis | Module List :
BSU16170 codY

transcriptional repressor CodY (RefSeq)

CircVis
Functional Annotations (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16170
(Mouseover regulator name to see its description)

BSU16170 is regulated by 14 influences and regulates 25 modules.
Regulators for BSU16170 codY (14)
Regulator Module Operator
BSU04460 170 tf
BSU14990 170 tf
BSU16170 170 tf
BSU24250 170 tf
BSU28400 170 tf
BSU32870 170 tf
BSU35520 170 tf
BSU35840 170 tf
BSU15640 167 tf
BSU16170 167 tf
BSU16810 167 tf
BSU35650 167 tf
BSU38600 167 tf
BSU39430 167 tf
Regulated by BSU16170 (25)
Module Residual Genes
3 0.30 15
55 0.51 26
103 0.26 14
119 0.36 19
120 0.28 19
167 0.48 12
170 0.44 28
197 0.45 26
204 0.31 18
211 0.31 17
212 0.38 15
221 0.39 16
227 0.32 18
248 0.46 7
272 0.37 21
273 0.41 24
283 0.45 5
284 0.50 7
288 0.36 19
290 0.42 6
292 0.47 22
314 0.33 23
329 0.46 26
350 0.47 24
374 0.29 16
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5282 6.10e+00 cTtCATtgTagCATgtcGaGcTtc
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5283 1.50e+01 CgCctCCGgGtAAAAgGgtgGAgA
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5288 3.90e+02 tctTTtTTCgtctGgtcag
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5289 3.60e+02 aCtg.TTTTTT
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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 BSU16170

BSU16170 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
Module neighborhood information for BSU16170

BSU16170 has total of 39 gene neighbors in modules 167, 170
Gene neighbors (39)
Gene Common Name Description Module membership
BSU02180 ybfE hypothetical protein (RefSeq) 163, 167
BSU04570 murF UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanine ligase (RefSeq) 170, 409
BSU05750 ydhG hypothetical protein (RefSeq) 166, 167
BSU08020 yfjO putative RNA methyltransferase (RefSeq) 170, 191
BSU09110 yhcJ putative ABC transporter (binding lipoprotein) (RefSeq) 128, 167
BSU09510 yhdL negative regulator of the activity of sigma-M (RefSeq) 38, 170
BSU10760 yisL hypothetical protein (RefSeq) 167, 313
BSU11580 yjbK putative RNA/thiamine triphosphatase (RefSeq) 116, 167
BSU13920 splA TRAP-like transcriptional regulator (RefSeq) 170, 274
BSU14090 ykuI hypothetical protein (RefSeq) 167, 274
BSU14440 ykpB 2-dehydropantoate 2-reductase (RefSeq) 170, 173
BSU14630 speA arginine decarboxylase (RefSeq) 51, 170
BSU14990 ylbF putative regulatory protein (RefSeq) 159, 170
BSU15150 ftsL cell-division protein (RefSeq) 170, 377
BSU15160 pbpB penicillin-binding protein 2B (RefSeq) 170, 377
BSU15240 divIB cell-division initiation protein (RefSeq) 170, 228
BSU15250 ylxW hypothetical protein (RefSeq) 170, 228
BSU16170 codY transcriptional repressor CodY (RefSeq) 167, 170
BSU16640 ylxP hypothetical protein (RefSeq) 170, 292
BSU19100 yobV putative transcriptional regulator (RefSeq) 64, 170
BSU19170 yocD putative carboxypeptidase (RefSeq) 51, 170
BSU21710 dinF damage inducible, Na+ driven multidrug efflux pump (RefSeq) 67, 170
BSU21720 ypmT hypothetical protein (RefSeq) 116, 170
BSU21760 ypmP hypothetical protein (RefSeq) 36, 167
BSU21800 ypkP putative acyltransferase (RefSeq) 53, 170
BSU24840 yqgS putative anion transporter and exported enzyme (RefSeq) 97, 170
BSU25310 dgkA undecaprenol kinase (RefSeq) 170, 193
BSU25330 yqfF putative membrane associate hydrolase (RefSeq) 170, 221
BSU25640 nadD nicotinic acid mononucleotide adenylyltransferase (RefSeq) 166, 170
BSU25660 aroE shikimate 5-dehydrogenase (RefSeq) 166, 170
BSU26610 yrkA putative membrane associated protein (RefSeq) 159, 170
BSU27640 yrvC putative potassium transport accessory component (RefSeq) 170, 202
BSU27930 spo0B sporulation initiation phosphotransferase (RefSeq) 170, 292
BSU33850 yvbG putative integral inner membrane protein (RefSeq) 167, 296
BSU33860 yvbH hypothetical protein (RefSeq) 23, 167
BSU34170 ganR transcriptional regulator (LacI family) (RefSeq) 167, 293
BSU35840 ywtF putative transcriptional regulator (RefSeq) 159, 170
BSU36760 murAA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (RefSeq) 170, 325
BSU38880 yxjO putative transcriptional regulator (LysR family) (RefSeq) 167, 233
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 BSU16170
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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