Organism : Bacillus subtilis | Module List :
BSU11930 yjcO

putative DNA binding protein (RefSeq)

CircVis
Functional Annotations (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU11930
(Mouseover regulator name to see its description)

BSU11930 is regulated by 24 influences and regulates 8 modules.
Regulators for BSU11930 yjcO (24)
Regulator Module Operator
BSU00980 36 tf
BSU11930 36 tf
BSU16810 36 tf
BSU16900 36 tf
BSU18460 36 tf
BSU19050 36 tf
BSU19120 36 tf
BSU23100 36 tf
BSU26870 36 tf
BSU31680 36 tf
BSU35050 36 tf
BSU35430 36 tf
BSU35650 36 tf
BSU38910 36 tf
BSU01730 159 tf
BSU05120 159 tf
BSU11300 159 tf
BSU11930 159 tf
BSU13310 159 tf
BSU21780 159 tf
BSU23090 159 tf
BSU23100 159 tf
BSU35840 159 tf
BSU36440 159 tf

Warning: BSU11930 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
5032 4.00e+02 cGc.AtAaAa.Ga.gGCCt.Ga
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5033 1.10e+03 AAAGaGG
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5266 2.50e+03 C..TTtTttgT
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5267 4.60e+04 GaaGAaGgg.cTTT
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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 BSU11930

BSU11930 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Module neighborhood information for BSU11930

BSU11930 has total of 61 gene neighbors in modules 36, 159
Gene neighbors (61)
Gene Common Name Description Module membership
BSU00980 sigH RNA polymerase factor sigma-70 (RefSeq) 36, 145
BSU01730 sigW RNA polymerase sigma factor SigW (RefSeq) 159, 166
BSU01740 rsiW anti-sigma(W) factor (RefSeq) 159, 166
BSU05120 cspC cold-shock protein (RefSeq) 151, 159
BSU05200 ydeH putative integral inner membrane protein (RefSeq) 115, 159
BSU06270 ydjO hypothetical protein (RefSeq) 159, 266
BSU11300 med positive regulator of comK (RefSeq) 14, 159
BSU11430 oppA oligopeptide ABC transporter (binding lipoprotein) (RefSeq) 36, 261
BSU11920 yjcN hypothetical protein (RefSeq) 36, 159
BSU11930 yjcO putative DNA binding protein (RefSeq) 36, 159
BSU12040 yjdG putative acetyltransferase (RefSeq) 49, 159
BSU13320 ykzB hypothetical protein (RefSeq) 159, 216
BSU14540 ykzG hypothetical protein (RefSeq) 36, 145
BSU14570 ykyA putative chromosome partitioning protein (RefSeq) 36, 145
BSU14760 ylaF hypothetical protein (RefSeq) 36, 145
BSU14990 ylbF putative regulatory protein (RefSeq) 159, 170
BSU15000 ylbG hypothetical protein (RefSeq) 7, 36
BSU17060 ymzD putative integral inner membrane protein (RefSeq) 115, 159
BSU17230 pksS cytochrome P450 of bacillaene metabolism (RefSeq) 36, 159
BSU18650 pelB pectin lyase (RefSeq) 159, 179
BSU18870 yozI hypothetical protein (RefSeq) 36, 274
BSU18910 rapK response regulator aspartate phosphatase (RefSeq) 36, 302
BSU18980 yobJ hypothetical protein (RefSeq) 159, 166
BSU19290 yozO hypothetical protein (RefSeq) 36, 166
BSU21670 BSU21670 None 25, 159
BSU21760 ypmP hypothetical protein (RefSeq) 36, 167
BSU21780 yplP transcriptional enhancer (RefSeq) 159, 226
BSU22020 ypbS hypothetical protein (RefSeq) 36, 105
BSU22810 yphF putative lipoprotein (RefSeq) 36, 105
BSU22820 yphE hypothetical protein (RefSeq) 36, 105
BSU22900 ypfB hypothetical protein (RefSeq) 36, 193
BSU23090 rsiX negative regulator of sigma(X) activity (RefSeq) 145, 159
BSU23100 sigX RNA polymerase sigma factor SigX (RefSeq) 145, 159
BSU23310 sipS type I signal peptidase (RefSeq) 94, 159
BSU23720 yqzH hypothetical protein (RefSeq) 159, 270
BSU23730 yqjV putative efflux transporter (RefSeq) 36, 159
BSU23740 yqjU hypothetical protein (RefSeq) 36, 291
BSU25090 yqfW putative nucleotidase (RefSeq) 151, 159
BSU25560 holA DNA polymerase III subunit delta (RefSeq) 151, 159
BSU25690 sda check point factor coupling initiation of sporulation and replication initiation (RefSeq) 36, 159
BSU25700 yqeF putative lipoprotein; putative esterase (RefSeq) 121, 159
BSU26610 yrkA putative membrane associated protein (RefSeq) 159, 170
BSU26760 yrdC putative hydrolase (RefSeq) 28, 36
BSU31450 kinB two-component sensor histidine kinase (RefSeq) 36, 105
BSU33210 yvrG two-component sensor histidine kinase YvrG innvolved in cell wall processes [YvrH] (RefSeq) 36, 247
BSU33890 yvbK putative acyltransferase (RefSeq) 36, 145
BSU35840 ywtF putative transcriptional regulator (RefSeq) 159, 170
BSU38860 galE UDP-glucose 4-epimerase (RefSeq) 36, 145
BSU39010 yxjB putative ribosomal RNA methyltransferase (RefSeq) 51, 159
BSU39240 yxxF putative transporter (RefSeq) 159, 350
BSU40140 yydJ putative permease for export of a regulatory peptide (RefSeq) 36, 115
BSU40160 yydH putative membrane metalloprotease (RefSeq) 36, 306
BSU40200 yydD hypothetical protein (RefSeq) 36, 145
BSU40210 yydC hypothetical protein (RefSeq) 36, 145
BSU40220 yydB putative phosphohydrolase (RefSeq) 36, 145
BSU40230 yydA rRNA large subunit methyltransferase (RefSeq) 36, 70
BSU40470 yycC hypothetical protein (RefSeq) 159, 191
BSU40480 yycB putative anion ABC transporter (permease) (RefSeq) 159, 191
BSU40580 yybN hypothetical protein (RefSeq) 36, 162
BSU40590 yybM putative integral inner membrane protein (RefSeq) 36, 162
BSU40650 yybG hypothetical protein (RefSeq) 36, 116
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 BSU11930
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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