Organism : Bacillus subtilis | Module List :
BSU06580 yerC

hypothetical protein (RefSeq)

CircVis
Functional Annotations (6)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
yecD_yerC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU06580
(Mouseover regulator name to see its description)

BSU06580 is regulated by 15 influences and regulates 5 modules.
Regulators for BSU06580 yerC (15)
Regulator Module Operator
BSU05330 161 tf
BSU05850 161 tf
BSU07390 161 tf
BSU09480 161 tf
BSU19200 161 tf
BSU25100 161 tf
BSU29000 161 tf
BSU40010 161 tf
BSU02160 174 tf
BSU05970 174 tf
BSU06140 174 tf
BSU09480 174 tf
BSU09830 174 tf
BSU26220 174 tf
BSU40800 174 tf

Warning: BSU06580 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
5270 1.40e-03 ca.CagCcggC
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5271 2.50e-01 AAaGTaCGTaCtTTTa.TtcT
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5296 3.00e-03 tTtTCcctTTTAcA
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5297 1.10e+01 cCTTgTTTTTTtATGc
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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 BSU06580

BSU06580 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
yecD_yerC tigr/ tigrfam
Module neighborhood information for BSU06580

BSU06580 has total of 48 gene neighbors in modules 161, 174
Gene neighbors (48)
Gene Common Name Description Module membership
BSU01520 ybaK putative alkylated deoxynucleotide triphosphohydrolase (RefSeq) 129, 174
BSU01890 ybcL putative efflux transporter (RefSeq) 161, 405
BSU03020 ycgA putative integral inner membrane protein (RefSeq) 157, 161
BSU04230 ydaH putative integral inner membrane protein (RefSeq) 161, 177
BSU05300 ydeQ putative NAD(P)H oxidoreductase (RefSeq) 151, 161
BSU05330 aseR transcriptional regulator (metals sensing ArsR-SmtB repressors family) (RefSeq) 14, 161
BSU05380 ydfE putative flavoprotein (RefSeq) 174, 239
BSU06580 yerC hypothetical protein (RefSeq) 161, 174
BSU07390 yfmP transcriptional regulator (MerR family) of metal efflux transporter expression (RefSeq) 161, 258
BSU07400 yfmO metal efflux transporter (RefSeq) 161, 270
BSU07830 yfkO NAD(P)H-flavin oxidoreductase (RefSeq) 19, 161
BSU07840 yfkN bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein (RefSeq) 33, 174
BSU08800 ygaK putative FAD-dependent oxido-reductase (RefSeq) 161, 174
BSU11090 yitR hypothetical protein (RefSeq) 71, 161
BSU12090 cotT spore coat protein (inner coat) (RefSeq) 174, 263
BSU13040 hmp nitric oxide dioxygenase (RefSeq) 174, 178
BSU14950 ylbB putative oxidoreductase (RefSeq) 14, 161
BSU18280 yngK hypothetical protein (RefSeq) 174, 280
BSU18810 yobA hypothetical protein (RefSeq) 161, 379
BSU20200 yorZ hypothetical protein; phage SPbeta (RefSeq) 174, 376
BSU20320 yorN hypothetical protein; phage SPbeta (RefSeq) 174, 376
BSU20430 yorC hypothetical protein; phage SPbeta (RefSeq) 174, 337
BSU20980 yonV conserved hypothetical protein; phage SPbeta (RefSeq) 174, 376
BSU21310 yozP hypothetical protein; phage SPbeta (RefSeq) 174, 307
BSU23700 yqjX hypothetical protein (RefSeq) 161, 270
BSU23710 yqjW DNA polymerase IV (RefSeq) 161, 270
BSU25010 yqgE putative efflux transporter (RefSeq) 174, 294
BSU25780 arsC arsenate reductase (RefSeq) 161, 249
BSU26640 yrdP putative oxidoreductase (RefSeq) 19, 161
BSU26650 czcD potassium/proton-divalent cation antiporter (RefSeq) 19, 161
BSU27120 sigV RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma(V)) (RefSeq) 74, 174
BSU27130 rsiV anti-sigma(V) factor (RefSeq) 74, 174
BSU27420 yrrI putative permease (RefSeq) 174, 231
BSU27540 yrvM putative enzyme of sulfur-containing coenzyme synthesis (RefSeq) 51, 161
BSU28680 glcD glycolate oxidase subunit (RefSeq) 174, 405
BSU28690 glcF glycolate oxidase iron-sulfur subunit (RefSeq) 174, 405
BSU29030 ytcD putative transcriptional regulator (MarD family) (RefSeq) 157, 161
BSU29040 ytbD putative transporter (RefSeq) 4, 161
BSU29050 ytbE putative aldo/keto reductase (RefSeq) 4, 161
BSU33490 copB copper(I)-transporting ATPase (RefSeq) 161, 249
BSU34410 yveG hypothetical protein (RefSeq) 161, 241
BSU34420 yveF hypothetical protein (RefSeq) 174, 258
BSU34490 yvdS hypothetical protein (RefSeq) 174, 200
BSU34500 yvdR hypothetical protein (RefSeq) 174, 200
BSU35240 ctpB PDZ-containing carboxyl-terminal protease processing protease (RefSeq) 174, 367
BSU38350 ywbE hypothetical protein (RefSeq) 127, 161
BSU40010 yxaD putative transcriptional regulator (MarR family) (RefSeq) 161, 270
BSU40530 cotF spore coat protein (RefSeq) 96, 174
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 BSU06580
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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