Organism : Bacillus subtilis | Module List :
BSU03170 ycgK

putative transcriptional regulator (LysR family) (RefSeq)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03170
(Mouseover regulator name to see its description)

BSU03170 is regulated by 21 influences and regulates 6 modules.
Regulators for BSU03170 ycgK (21)
Regulator Module Operator
BSU03170 365 tf
BSU10880 365 tf
BSU11650 365 tf
BSU19050 365 tf
BSU19070 365 tf
BSU28410 365 tf
BSU29110 365 tf
BSU31070 365 tf
BSU33740 365 tf
BSU33840 365 tf
BSU34180 365 tf
BSU35430 365 tf
BSU37550 365 tf
BSU03170 80 tf
BSU13450 80 tf
BSU24020 80 tf
BSU27320 80 tf
BSU28820 80 tf
BSU29400 80 tf
BSU30020 80 tf
BSU40870 80 tf

Warning: BSU03170 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
5114 2.30e+03 CGTcCAAGA
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5115 5.10e+03 TcCTtCtTTTt
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5650 1.00e+02 caatAagGAG.tGgggaA
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5651 2.00e+04 TaAagGgGgtctTtc
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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 BSU03170

BSU03170 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU03170

BSU03170 has total of 40 gene neighbors in modules 80, 365
Gene neighbors (40)
Gene Common Name Description Module membership
BSU00240 csfB forespore-specific protein (RefSeq) 177, 365
BSU00730 cysK cysteine synthase (RefSeq) 80, 150
BSU02950 yceI putative transporter (RefSeq) 89, 365
BSU03160 ycgJ putative methyltransferase (RefSeq) 80, 341
BSU03170 ycgK putative transcriptional regulator (LysR family) (RefSeq) 80, 365
BSU03180 cah S-deacylase (RefSeq) 80, 261
BSU03190 ycgL hypothetical protein (RefSeq) 80, 185
BSU03280 nasF uroporphyrin-III C-methyltransferase (RefSeq) 80, 87
BSU03790 yclM aspartate kinase (RefSeq) 11, 365
BSU04140 pbpC penicillin-binding lipoprotein 3 (RefSeq) 80, 245
BSU04520 ydbM putative acyl-CoA dehydrogenase (RefSeq) 80, 356
BSU07200 yetJ putative integral inner membrane protein (RefSeq) 60, 80
BSU07700 nagP phosphotransferase system (PTS) N-acetylglucosamine-specific enzyme IICB component (RefSeq) 38, 365
BSU08640 yfhS hypothetical protein (RefSeq) 163, 365
BSU09130 tcyP sodium-cystine symporter (RefSeq) 80, 190
BSU12470 yjqA conserved hypothetical protein; PBSX phage (RefSeq) 322, 365
BSU13140 ohrA peroxiredoxin (RefSeq) 80, 365
BSU14200 ykuS hypothetical protein (RefSeq) 11, 365
BSU15340 ylmA putative ABC transporter (ATP-binding protein) (RefSeq) 365, 393
BSU16845 BSU16845 None 80, 215
BSU19080 yobT putative metal-dependent hydrolase (RefSeq) 327, 365
BSU19350 yocS putative sodium-dependent transporter (RefSeq) 157, 365
BSU22850 seaA hypothetical protein (RefSeq) 274, 365
BSU22860 yphA putative integral inner membrane protein (RefSeq) 257, 365
BSU27200 yrhG putative formate/nitrite transporter (RefSeq) 80, 102
BSU27250 yrhB cystathionine beta-lyase (RefSeq) 80, 150
BSU27260 mccA cystathionine beta-synthase for the reverse transsulfuration pathway (RefSeq) 80, 150
BSU31790 yueG putative spore germination protein (RefSeq) 233, 365
BSU32050 yuiE leucyl aminopeptidase (RefSeq) 80, 255
BSU36620 ywnB putative oxidoreductase (RefSeq) 37, 365
BSU39450 yxeR putative ethanolamine transporter (RefSeq) 80, 276
BSU39460 yxeQ putative catabolic enzyme (RefSeq) 80, 276
BSU39470 yxeP putative amidohydrolase (RefSeq) 80, 144
BSU39480 yxeO putative ABC transporter (ATP-binding protein) (RefSeq) 80, 144
BSU39490 yxeN putative ABC transporter (permease) (RefSeq) 80, 144
BSU39500 yxeM putative ABC transporter (binding lipoprotein) (RefSeq) 80, 144
BSU39510 yxeL putative acetyltransferase (RefSeq) 80, 276
BSU39520 yxeK putative monooxygenase (RefSeq) 80, 144
BSU40550 ppaC putative manganese-dependent inorganic pyrophosphatase (RefSeq) 80, 247
BSU40660 yybF putative permease (RefSeq) 335, 365
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 BSU03170
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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