Organism : Bacillus subtilis | Module List :
BSU03370 yckA

putative ABC transporter (permease) (RefSeq)

CircVis
Functional Annotations (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
HEQRo_perm_3TM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03370
(Mouseover regulator name to see its description)

BSU03370 is regulated by 13 influences and regulates 0 modules.
Regulators for BSU03370 yckA (13)
Regulator Module Operator
BSU03470 98 tf
BSU10420 98 tf
BSU35430 98 tf
BSU36300 98 tf
BSU40050 98 tf
BSU01010 266 tf
BSU04650 266 tf
BSU09510 266 tf
BSU13210 266 tf
BSU23090 266 tf
BSU28410 266 tf
BSU35840 266 tf
BSU37160 266 tf

Warning: BSU03370 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
5150 8.60e-03 aAaAAagCatg
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5151 3.70e+02 GGAGG.aA
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5472 2.20e+02 ggaGGAGGtGaaAg
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5473 3.70e+04 AgAaAGGgaGtggCa
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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 BSU03370

BSU03370 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
HEQRo_perm_3TM tigr/ tigrfam
Module neighborhood information for BSU03370

BSU03370 has total of 49 gene neighbors in modules 98, 266
Gene neighbors (49)
Gene Common Name Description Module membership
BSU02010 ybdK two-component sensor histidine kinase [YbdJ] (RefSeq) 98, 394
BSU03370 yckA putative ABC transporter (permease) (RefSeq) 98, 266
BSU03380 yckB putative ABC transporter (binding lipoprotein) (RefSeq) 98, 266
BSU03800 yclN putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03810 yclO putative iron-siderophore ABC transporter (permease) (RefSeq) 93, 266
BSU03820 yclP putative iron-siderophore ABC transporter (ATP-binding protein) (RefSeq) 93, 266
BSU03830 yclQ putative iron-siderophore ABC transporter (binding lipoprotein) (RefSeq) 93, 266
BSU04580 cshA ATP-dependent RNA helicase; cold shock (RefSeq) 266, 322
BSU04650 endB antitoxin MazF (RefSeq) 212, 266
BSU04660 ndoA endoribonuclease toxin (RefSeq) 212, 266
BSU06270 ydjO hypothetical protein (RefSeq) 159, 266
BSU06830 rapH response regulator aspartate phosphatase (RefSeq) 98, 394
BSU09100 cspB major cold-shock protein, RNA helicase co-factor, RNA co-chaperone (RefSeq) 266, 322
BSU10420 comK competence transcription factor (CTF) (RefSeq) 98, 394
BSU12280 rex transcriptional repressor of the rex ndh operon (RefSeq) 119, 266
BSU12290 ndh NADH dehydrogenase (RefSeq) 119, 266
BSU16110 dprA DNA processing Smf single strand binding protein (RefSeq) 96, 98
BSU16940 recA recombinase A (RefSeq) 7, 98
BSU16960 ymdA phosphodiesterase (RefSeq) 107, 266
BSU18300 ppsE plipastatin synthetase (RefSeq) 98, 150
BSU18310 ppsD plipastatin synthetase (RefSeq) 98, 306
BSU22780 folE GTP cyclohydrolase I (RefSeq) 228, 266
BSU23370 ypuA hypothetical protein (RefSeq) 7, 266
BSU25160 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (RefSeq) 226, 266
BSU25400 yqeY hypothetical protein (RefSeq) 7, 266
BSU25410 rpsU 30S ribosomal protein S21 (RefSeq) 7, 266
BSU25570 comEC DNA channel for uptake in competent cells (RefSeq) 98, 394
BSU25580 comEB putative enzyme associated to DNA transport (competence) (RefSeq) 98, 394
BSU27580 yrvJ putative N-acetylmuramoyl-L-alanine amidase, family 3 (RefSeq) 266, 322
BSU27990 minD ATPase activator of MinC (RefSeq) 212, 266
BSU28040 radC DNA repair protein RadC (RefSeq) 98, 266
BSU28050 maf Maf-like protein (RefSeq) 98, 266
BSU28070 comC membrane protease and transmethylase (RefSeq) 98, 394
BSU28470 lysC aspartate kinase (RefSeq) 266, 300
BSU29805 BSU29805 None 98, 169
BSU33870 yvbI putative permease (RefSeq) 197, 266
BSU35450 comFC putative component of the DNA transport apparatus (RefSeq) 98, 394
BSU35460 comFB hypothetical protein (RefSeq) 98, 394
BSU35760 tagB teichoic acid primase, CDP-glycerol:N-acetyl-beta-d-mannosaminyl-1, 4-N-acetyl-d-glucosaminyldiphosphoundecaprenyl glycerophosphotransferase (RefSeq) 226, 266
BSU37160 rpoE DNA-directed RNA polymerase subunit delta (RefSeq) 197, 266
BSU37630 ywfM putative transporter (RefSeq) 98, 241
BSU38410 sacX negative regulator of SacY (RefSeq) 98, 291
BSU38850 yxkC hypothetical protein (RefSeq) 7, 98
BSU40920 yyaF GTP-dependent nucleic acid-binding protein EngD (RefSeq) 98, 266
BSU41060 rpmH 50S ribosomal protein L34 (RefSeq) 119, 266
VIMSS37375 VIMSS37375 None 98, 117
VIMSS39235 VIMSS39235 None 69, 98
VIMSS39516 VIMSS39516 None 98, 187
VIMSS39733 VIMSS39733 None 69, 98
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 BSU03370
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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