Organism : Bacillus subtilis | Module List :
BSU05580 ydgC

putative transcriptional regulator (RefSeq)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
carbohydrate metabolic process go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU05580
(Mouseover regulator name to see its description)

BSU05580 is regulated by 30 influences and regulates 7 modules.
Regulators for BSU05580 ydgC (30)
Regulator Module Operator
BSU00830 111 tf
BSU01730 111 tf
BSU05370 111 tf
BSU05580 111 tf
BSU05850 111 tf
BSU09430 111 tf
BSU13150 111 tf
BSU15690 111 tf
BSU24320 111 tf
BSU27110 111 tf
BSU33230 111 tf
BSU33580 111 tf
BSU36110 111 tf
BSU36160 111 tf
BSU37550 111 tf
BSU38420 111 tf
BSU40540 111 tf
BSU04680 262 tf
BSU05370 262 tf
BSU05580 262 tf
BSU05670 262 tf
BSU09380 262 tf
BSU09500 262 tf
BSU09560 262 tf
BSU10880 262 tf
BSU23100 262 tf
BSU27110 262 tf
BSU31530 262 tf
BSU36020 262 tf
BSU40540 262 tf

Warning: BSU05580 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
5176 6.30e+01 tttttaAA.aGAggaaaa.aG
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5177 3.10e+02 A.A.agaAag..Ggc
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5464 1.80e-02 tcatttgCTGcCaGa
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5465 7.00e+02 C.TgCCtcCaggcC
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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 BSU05580

BSU05580 is enriched for 7 functions in 3 categories.
Module neighborhood information for BSU05580

BSU05580 has total of 43 gene neighbors in modules 111, 262
Gene neighbors (43)
Gene Common Name Description Module membership
BSU00180 tadA tRNA specific adenosine deaminase (RefSeq) 111, 123
BSU03030 ycgB putative integral inner membrane protein (RefSeq) 262, 412
BSU05370 ydfD putative PLP-dependent transcriptional regulator (RefSeq) 262, 378
BSU05580 ydgC putative transcriptional regulator (RefSeq) 111, 262
BSU05590 ydgD hypothetical protein (RefSeq) 111, 262
BSU05600 ydgE putative N-acetyltransferase (RefSeq) 111, 216
BSU05610 vmlR ATP-binding cassette efflux transporter (RefSeq) 111, 354
BSU05660 ydgI putative dehydrogenase (RefSeq) 123, 262
BSU05670 ydgJ putative transcriptional regulator (MarR family) (RefSeq) 123, 262
BSU06060 ydiO DNA-methyltransferase (cytosine-specific) (RefSeq) 83, 262
BSU07680 yflH hypothetical protein (RefSeq) 262, 373
BSU07735 BSU07735 None 111, 262
BSU08680 ygaC hypothetical protein (RefSeq) 262, 354
BSU08890 ygaO putative integral inner membrane protein (RefSeq) 262, 378
BSU10480 yhjE putative integral inner membrane protein (RefSeq) 123, 262
BSU10490 sipV type I signal peptidase (RefSeq) 123, 262
BSU10890 yisX hypothetical protein (RefSeq) 111, 262
BSU13150 ohrR transcriptional regulator sensing organic peroxides (RefSeq) 111, 123
BSU13850 zosA Zn transporter (RefSeq) 111, 249
BSU14040 ykuD murein transglycosylase (RefSeq) 262, 378
BSU14050 ykuE putative metallophosphoesterase (RefSeq) 262, 378
BSU15060 ylbM hypothetical protein (RefSeq) 111, 123
BSU19560 yodD putative hydrolase (RefSeq) 50, 111
BSU19570 yodE putative lyase/dioxygenase (RefSeq) 50, 111
BSU21870 ilvD dihydroxy-acid dehydratase (RefSeq) 28, 111
BSU23640 yqkD putative hydrolase (RefSeq) 111, 373
BSU28490 uvrC excinuclease ABC subunit C (RefSeq) 244, 262
BSU29640 ytsP hypothetical protein (RefSeq) 82, 262
BSU32770 yusE putative thiol-disulfide oxidoreductase with thioredoxin domain (RefSeq) 111, 354
BSU32960 yusY hypothetical protein (RefSeq) 31, 262
BSU33230 sigO alternative sigma factor (RefSeq) 111, 341
BSU33560 yvaD putative integral inner membrane protein (RefSeq) 111, 318
BSU33570 yvaE putative metabolite-efflux transporter (RefSeq) 111, 318
BSU33580 yvaF putative transcriptional regulator (RefSeq) 111, 318
BSU33980 yvbT putative alkanal monooxygenase (RefSeq) 262, 378
BSU37540 ywhB 4-oxalocrotonate tautomerase (RefSeq) 111, 115
BSU37550 ywhA putative transcriptional regulator (MarR family) (RefSeq) 111, 123
BSU37960 ywdH putative aldehyde dehydrogenase (RefSeq) 111, 243
BSU37990 ywdE putative integral inner membrane protein (RefSeq) 38, 111
BSU38000 ywdD putative integral inner membrane protein (RefSeq) 38, 111
BSU38290 thiE thiamine-phosphate pyrophosphorylase (RefSeq) 37, 262
BSU38300 thiM hydroxyethylthiazole kinase (RefSeq) 37, 262
VIMSS39315 VIMSS39315 None 215, 262
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 BSU05580
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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