Organism : Bacillus subtilis | Module List :
BSU25130 yqfS

endonuclease IV (RefSeq)

CircVis
Functional Annotations (7)
Function System
Endonuclease IV cog/ cog
DNA binding go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
deoxyribonuclease IV (phage-T4-induced) activity go/ molecular_function
Base excision repair kegg/ kegg pathway
nfo tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU25130
(Mouseover regulator name to see its description)

BSU25130 is regulated by 23 influences and regulates 0 modules.
Regulators for BSU25130 yqfS (23)
Regulator Module Operator
BSU00700 204 tf
BSU01010 204 tf
BSU01070 204 tf
BSU01080 204 tf
BSU02220 204 tf
BSU02680 204 tf
BSU02970 204 tf
BSU10860 204 tf
BSU16170 204 tf
BSU16600 204 tf
BSU16810 204 tf
BSU35520 204 tf
BSU01010 191 tf
BSU12370 191 tf
BSU12510 191 tf
BSU16810 191 tf
BSU17080 191 tf
BSU21780 191 tf
BSU28820 191 tf
BSU31680 191 tf
BSU32870 191 tf
BSU33790 191 tf
BSU40990 191 tf

Warning: BSU25130 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
5328 1.20e+02 AaAAGAGaGcAtgG
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5329 1.30e+03 tcTgcaTCagtgtCtgcgcgaTTa
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5352 2.90e+01 TtCagCaGCt
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5353 2.90e+03 AAaAaaacC.gaTgagaaAGG
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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 BSU25130

BSU25130 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Endonuclease IV cog/ cog
DNA binding go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
deoxyribonuclease IV (phage-T4-induced) activity go/ molecular_function
Base excision repair kegg/ kegg pathway
nfo tigr/ tigrfam
Module neighborhood information for BSU25130

BSU25130 has total of 44 gene neighbors in modules 191, 204
Gene neighbors (44)
Gene Common Name Description Module membership
BSU00020 dnaN DNA polymerase III subunit beta (RefSeq) 34, 204
BSU01000 secE preprotein translocase subunit SecE (RefSeq) 191, 226
BSU06620 ligA NAD-dependent DNA ligase LigA (RefSeq) 204, 211
BSU08020 yfjO putative RNA methyltransferase (RefSeq) 170, 191
BSU12370 exuR transcriptional regulator (LacI family) (RefSeq) 35, 191
BSU12510 xre Phage PBSX transcriptional regulator (RefSeq) 191, 258
BSU17080 pksA putative transcriptional regulator (RefSeq) 191, 258
BSU19340 yocR putative sodium-dependent transporter (RefSeq) 116, 191
BSU21790 yplQ putative membrane hydrolase (RefSeq) 51, 191
BSU22840 engA GTP-binding protein EngA (RefSeq) 204, 211
BSU23250 ribH 6,7-dimethyl-8-ribityllumazine synthase (RefSeq) 97, 191
BSU23260 ribA bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein (RefSeq) 97, 191
BSU23270 ribE riboflavin synthase subunit alpha (RefSeq) 97, 191
BSU23280 ribD fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase (RefSeq) 97, 191
BSU23380 lysA diaminopimelate decarboxylase (RefSeq) 191, 322
BSU25130 yqfS endonuclease IV (RefSeq) 191, 204
BSU25140 cshB ATP-dependent RNA helicase; cold shock (RefSeq) 204, 225
BSU25210 dnaG DNA primase (RefSeq) 191, 309
BSU25280 recO DNA repair protein RecO (RefSeq) 97, 191
BSU25500 hemN coproporphyrinogen III oxidase (RefSeq) 34, 204
BSU25510 lepA GTP-binding protein LepA (RefSeq) 204, 409
BSU25620 yqeL hypothetical protein (RefSeq) 204, 374
BSU25630 yqeK putative hydrolase (RefSeq) 204, 374
BSU25650 yqeI putative RNA-binding protein (RefSeq) 204, 374
BSU27610 apt adenine phosphoribosyltransferase (RefSeq) 119, 204
BSU27910 pheB hypothetical protein (RefSeq) 191, 221
BSU29790 murC UDP-N-acetylmuramate--L-alanine ligase (RefSeq) 204, 265
BSU30480 ytqA putative Fe-S oxidoreductase (RefSeq) 191, 265
BSU31322 BSU31322 None 45, 204
BSU31875 BSU31875 None 204, 265
BSU32740 metP methionine ABC transporter, permease component (RefSeq) 139, 191
BSU32750 metQ methionine ABC transporter (ATP-binding protein) (RefSeq) 139, 191
BSU33110 liaG conserved hypothetical protein (response to antibiotic stress) (RefSeq) 23, 191
BSU33780 sdpI integral inner membrane regulator of autophagy (RefSeq) 191, 258
BSU33790 sdpR transcriptional regulator (ArsR family) (RefSeq) 191, 258
BSU35710 tagG teichoic acid precursors permease (RefSeq) 204, 397
BSU35720 tagF CDP-glycerol:polyglycerol phosphate glycero-phosphotransferase (poly(glycerol phosphate) polymerase) (RefSeq) 204, 374
BSU40470 yycC hypothetical protein (RefSeq) 159, 191
BSU40480 yycB putative anion ABC transporter (permease) (RefSeq) 159, 191
BSU40990 noc DNA-binding protein Spo0J-like (RefSeq) 191, 228
VIMSS36736 VIMSS36736 None 191, 249
VIMSS37174 VIMSS37174 None 122, 204
VIMSS39181 VIMSS39181 None 204, 235
VIMSS39309 VIMSS39309 None 90, 191
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 BSU25130
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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