Organism : Bacillus subtilis | Module List :
BSU12880 ykcB

putative integral membrane protein; putative glycosyl transferase (RefSeq)

CircVis
Functional Annotations (3)
Function System
mannosyltransferase activity go/ molecular_function
protein O-linked glycosylation go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU12880
(Mouseover regulator name to see its description)

BSU12880 is regulated by 20 influences and regulates 0 modules.
Regulators for BSU12880 ykcB (20)
Regulator Module Operator
BSU01430 238 tf
BSU09500 238 tf
BSU10880 238 tf
BSU26320 238 tf
BSU27000 238 tf
BSU35520 238 tf
BSU37290 238 tf
BSU02000 130 tf
BSU03560 130 tf
BSU05420 130 tf
BSU06960 130 tf
BSU08300 130 tf
BSU25200 130 tf
BSU26220 130 tf
BSU26320 130 tf
BSU26340 130 tf
BSU36600 130 tf
BSU37290 130 tf
BSU39850 130 tf
BSU40800 130 tf

Warning: BSU12880 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
5212 6.90e+00 TCCCcTTTc.cgac
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5213 3.70e+01 CtcTtCgcgaCaaCTtTaTCcAAC
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5418 2.90e-01 TaTTcAttttCaaAA
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5419 3.90e-01 aagAaacaaTT.AcAAttaA
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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 BSU12880

BSU12880 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
mannosyltransferase activity go/ molecular_function
protein O-linked glycosylation go/ biological_process
membrane go/ cellular_component
Module neighborhood information for BSU12880

BSU12880 has total of 49 gene neighbors in modules 130, 238
Gene neighbors (49)
Gene Common Name Description Module membership
BSU02690 ansZ L-asparaginase (putative lipoprotein) (RefSeq) 130, 200
BSU02730 natK two-component sensor histidine kinase [NatR] (RefSeq) 130, 246
BSU02740 natR two-component response regulator [NatK] (RefSeq) 130, 246
BSU02750 natA Na+ ABC efflux transporter (ATP-binding protein) (RefSeq) 130, 246
BSU02760 natB Na+ ABC efflux transporter (permease) (RefSeq) 130, 246
BSU03050 ldh L-lactate dehydrogenase (RefSeq) 238, 406
BSU03060 lctP L-lactate permease (RefSeq) 178, 238
BSU03310 nasC assimilatory nitrate reductase (catalytic subunit) (RefSeq) 130, 405
BSU03330 nasA nitrate transporter (RefSeq) 130, 405
BSU06550 yecA putative amino acid/polyamine permease (RefSeq) 130, 301
BSU08240 catE catechol-2,3-dioxygenase subunit (RefSeq) 238, 307
BSU10590 yhjP hypothetical protein (RefSeq) 130, 371
BSU12880 ykcB putative integral membrane protein; putative glycosyl transferase (RefSeq) 130, 238
BSU12890 ykcC putative glycosyltransferase (RefSeq) 130, 291
BSU18820 yobB putative transcriptional regulator from bacteriophage (RefSeq) 217, 238
BSU25950 yqcC hypothetical protein (RefSeq) 130, 305
BSU25970 yqcA hypothetical protein (RefSeq) 130, 305
BSU25980 yqbT putative phage capsid assembly protein; skin element (RefSeq) 130, 305
BSU26000 yqbR conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26010 yqbQ conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26020 yqbP conserved hypothetical protein; skin element (RefSeq) 130, 305
BSU26030 yqbO putative lytic transglycosylase (RefSeq) 130, 305
BSU26060 yqbM hypothetical protein (RefSeq) 129, 130
BSU26090 yqbJ conserved hypothetical protein; skin element (RefSeq) 88, 130
BSU26100 yqbI conserved hypothetical protein; skin element (RefSeq) 130, 175
BSU26130 yqbF hypothetical protein; skin element (RefSeq) 129, 238
BSU26170 yqbB putative phage head morphogenesis protein; skin element (RefSeq) 130, 387
BSU26190 yqaT putative phage-related terminase large subunit; skin element (RefSeq) 238, 270
BSU26200 yqaS putative phage-related terminase small subunit; skin element (RefSeq) 238, 342
BSU26280 yqaK putative DNA recombination protein; skin element (RefSeq) 130, 371
BSU26290 yqaJ putative nuclease; skin element (RefSeq) 130, 371
BSU27010 adhA putative dehydrogenase (RefSeq) 238, 405
BSU31080 yuaB hypothetical protein (RefSeq) 217, 238
BSU31470 kapD sporulation inhibitor KapD (RefSeq) 238, 411
BSU31480 yuxJ putative exporter (RefSeq) 238, 341
BSU31580 maeN Na+/malate symporter (RefSeq) 64, 238
BSU34460 levB endolevanase (RefSeq) 130, 231
BSU35040 yvnB putative exported phosphohydrolase (RefSeq) 44, 238
BSU36500 ywoB putative integral inner membrane protein (RefSeq) 130, 307
BSU37050 ywkA malate dehydrogenase (RefSeq) 238, 406
BSU37250 narI nitrate reductase (gamma subunit) (RefSeq) 238, 405
BSU37260 narJ nitrate reductase (protein J) (RefSeq) 238, 405
BSU37270 narH nitrate reductase (beta subunit) (RefSeq) 238, 405
BSU37300 ywiC putative integral inner membrane protein (RefSeq) 29, 238
BSU37320 narK nitrite extrusion permease (RefSeq) 238, 405
BSU38390 ywbA putative phosphotransferase system enzyme IIC permease component (RefSeq) 44, 130
BSU40570 yybO putative permease (RefSeq) 130, 231
BSU40800 yyaN putative transcriptional regulator (MerR family) (RefSeq) 200, 238
BSU40810 yyaM putative efflux transporter (RefSeq) 200, 238
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 BSU12880
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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