Organism : Bacillus subtilis | Module List :
BSU04010 sipU

type I signal peptidase (RefSeq)

CircVis
Functional Annotations (6)
Function System
Signal peptidase I cog/ cog
proteolysis go/ biological_process
signal peptidase I activity go/ molecular_function
integral to membrane go/ cellular_component
Protein export kegg/ kegg pathway
sigpep_I_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU04010
(Mouseover regulator name to see its description)

BSU04010 is regulated by 38 influences and regulates 0 modules.
Regulators for BSU04010 sipU (38)
Regulator Module Operator
BSU05050 313 tf
BSU05420 313 tf
BSU07390 313 tf
BSU09330 313 tf
BSU09560 313 tf
BSU12560 313 tf
BSU19050 313 tf
BSU19540 313 tf
BSU23100 313 tf
BSU24020 313 tf
BSU24220 313 tf
BSU25250 313 tf
BSU25490 313 tf
BSU28820 313 tf
BSU29740 313 tf
BSU32870 313 tf
BSU33970 313 tf
BSU35430 313 tf
BSU37080 313 tf
BSU37160 313 tf
BSU00230 155 tf
BSU11500 155 tf
BSU15330 155 tf
BSU15690 155 tf
BSU18850 155 tf
BSU19050 155 tf
BSU23090 155 tf
BSU23100 155 tf
BSU23520 155 tf
BSU25760 155 tf
BSU28820 155 tf
BSU29740 155 tf
BSU30020 155 tf
BSU33840 155 tf
BSU33970 155 tf
BSU35650 155 tf
BSU36160 155 tf
BSU37580 155 tf

Warning: BSU04010 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
5258 6.50e+01 cggCagTTtCC
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5259 2.10e+03 GGagGA.atag
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5564 9.40e-04 AtaGGaGGAaa
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5565 6.30e+00 C.gatGGctgccgcg
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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 BSU04010

BSU04010 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Signal peptidase I cog/ cog
proteolysis go/ biological_process
signal peptidase I activity go/ molecular_function
integral to membrane go/ cellular_component
Protein export kegg/ kegg pathway
sigpep_I_bact tigr/ tigrfam
Module neighborhood information for BSU04010

BSU04010 has total of 49 gene neighbors in modules 155, 313
Gene neighbors (49)
Gene Common Name Description Module membership
BSU02260 ybfK carboxylesterase NP (RefSeq) 11, 155
BSU02700 estA secreted alkaliphilic lipase (RefSeq) 162, 313
BSU04010 sipU type I signal peptidase (RefSeq) 155, 313
BSU06190 ydjG putative phage replication protein (RefSeq) 162, 313
BSU06200 ydjH hypothetical protein (RefSeq) 162, 313
BSU09570 yhdR aspartate aminotransferase (RefSeq) 155, 247
BSU09890 natA Na+-efflux ABC transporter (ATP-binding protein) (RefSeq) 89, 313
BSU09900 natB Na+ exporter (ABC permease) (RefSeq) 89, 313
BSU10760 yisL hypothetical protein (RefSeq) 167, 313
BSU11170 yitY putative FMN/FAD-binding oxidoreductase (RefSeq) 155, 313
BSU11180 yitZ putative transport protein (RefSeq) 89, 313
BSU11620 yjbO pseudouridylate synthase (RefSeq) 155, 187
BSU14110 ykuK putative RNAse (RefSeq) 313, 385
BSU14180 dapH tetrahydrodipicolinate N-acetyltransferase (RefSeq) 253, 313
BSU14190 dapL N-acetyl-diaminopimelate deacetylase (RefSeq) 128, 313
BSU14350 yknX putative efflux permease (RefSeq) 162, 313
BSU14500 ykqA hypothetical protein (RefSeq) 155, 247
BSU14530 rnjA ribonuclease J1 (RefSeq) 135, 313
BSU15010 ylbH putative enzyme with adenosyl binding site (RefSeq) 313, 385
BSU15020 coaD phosphopantetheine adenylyltransferase (RefSeq) 313, 385
BSU15830 yloU hypothetical protein (RefSeq) 63, 155
BSU16080 ylqH putative flagellar biosynthesis protein (RefSeq) 7, 313
BSU16750 asd aspartate-semialdehyde dehydrogenase (RefSeq) 155, 334
BSU16780 rnjB ribonuclease J2 (RefSeq) 155, 289
BSU16950 pbpX penicillin-binding endopeptidase X (RefSeq) 313, 385
BSU18850 yobD transcriptional regulator (phage-related, Xre family) (RefSeq) 155, 202
BSU19630 deoD purine nucleoside phosphorylase (RefSeq) 289, 313
BSU21770 ilvA threonine dehydratase (RefSeq) 102, 155
BSU27650 secDF bifunctional preprotein translocase subunit SecD/SecF (RefSeq) 155, 273
BSU27900 pheA prephenate dehydratase (RefSeq) 199, 313
BSU28370 rph ribonuclease PH (RefSeq) 155, 187
BSU29740 ccpA transcriptional regulator (Lacl family) (RefSeq) 63, 155
BSU29930 amyX pullulanase (RefSeq) 255, 313
BSU29940 ytlR putative phospholipid kinase (RefSeq) 255, 313
BSU31150 yubB undecaprenyl pyrophosphate phosphatase (RefSeq) 116, 155
BSU33260 yvrN putative ABC transporter (ATP-binding protein) (RefSeq) 125, 155
BSU33270 yvrO putative ABC transporter (ATP-binding protein) (RefSeq) 125, 155
BSU33280 yvrP putative ABC transporter component (RefSeq) 125, 155
BSU33880 yvbJ hypothetical protein (RefSeq) 199, 313
BSU34020 yvbX putative epimerase modification of peptidoglycan (RefSeq) 247, 313
BSU34800 cwlO secreted cell wall DL-endopeptidase (RefSeq) 155, 273
BSU35480 yviA hypothetical protein (RefSeq) 145, 155
BSU37330 argS arginyl-tRNA synthetase (RefSeq) 102, 155
BSU39600 yxeC putative integral inner membrane protein (RefSeq) 302, 313
BSU40600 yybL putative integral inner membrane protein (RefSeq) 162, 313
BSU40610 yybK putative integral inner membrane protein (RefSeq) 162, 313
BSU40620 yybJ putative ATP-binding cassette protein (RefSeq) 162, 313
BSU41030 jag SpoIIIJ-associated RNA/ssDNA-binding protein (RefSeq) 313, 385
BSU41040 spoIIIJ OxaA-like protein precursor (RefSeq) 313, 385
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 BSU04010
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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