Organism : Bacillus cereus ATCC14579 | Module List :
BC1290

Phosphatidylglycerophosphatase B (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Membrane-associated phospholipid phosphatase cog/ cog
phosphatidylglycerophosphatase activity go/ molecular_function
membrane go/ cellular_component
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1290
(Mouseover regulator name to see its description)

BC1290 is regulated by 31 influences and regulates 0 modules.
Regulators for BC1290 (31)
Regulator Module Operator
BC0059 458 tf
BC0116 458 tf
BC0122 458 tf
BC0518 458 tf
BC0613 458 tf
BC1363 458 tf
BC1884 458 tf
BC2514 458 tf
BC2672 458 tf
BC2770 458 tf
BC3593 458 tf
BC3813 458 tf
BC3814 458 tf
BC3826 458 tf
BC4057 458 tf
BC5265 458 tf
BC0059 27 tf
BC0099 27 tf
BC0122 27 tf
BC0595 27 tf
BC1337 27 tf
BC1363 27 tf
BC2218 27 tf
BC2672 27 tf
BC2770 27 tf
BC3706 27 tf
BC3814 27 tf
BC3982 27 tf
BC4072 27 tf
BC5143 27 tf
BC5265 27 tf

Warning: BC1290 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
3976 3.10e+02 gataaGAgGagag
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3977 4.40e+02 AggaGCGCTtG
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4826 7.10e+01 ttGaaagGAgG
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4827 9.40e+01 ggc.CT.ttCCaTc
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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 BC1290

BC1290 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Membrane-associated phospholipid phosphatase cog/ cog
phosphatidylglycerophosphatase activity go/ molecular_function
membrane go/ cellular_component
hydrolase activity go/ molecular_function
Module neighborhood information for BC1290

BC1290 has total of 37 gene neighbors in modules 27, 458
Gene neighbors (37)
Gene Common Name Description Module membership
BC0021 BC0021 Deoxyguanosine kinase (NCBI ptt file) 69, 458
BC0219 BC0219 Glucose uptake protein homolog (NCBI ptt file) 27, 499
BC0481 BC0481 Glutaminase (NCBI ptt file) 27, 133
BC1227 BC1227 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 27, 341
BC1289 BC1289 Spermidine/putrescine-binding protein (NCBI ptt file) 388, 458
BC1290 BC1290 Phosphatidylglycerophosphatase B (NCBI ptt file) 27, 458
BC1357 BC1357 ABC transporter ATP-binding protein (NCBI ptt file) 27, 75
BC1358 BC1358 ABC transporter permease protein (NCBI ptt file) 27, 341
BC1473 BC1473 ResA protein (NCBI ptt file) 27, 479
BC1499 BC1499 Isopentenyl-diphosphate delta-isomerase (NCBI ptt file) 27, 161
BC1565 BC1565 ATP-dependent helicase, DinG family (NCBI ptt file) 92, 458
BC2907 BC2907 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 479
BC3183 BC3183 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 499
BC3229 BC3229 hypothetical Membrane Spanning Protein (NCBI ptt file) 27, 304
BC3911 BC3911 Cell division protein ftsW (NCBI ptt file) 312, 458
BC4077 BC4077 Acetoin transport ATP-binding protein (NCBI ptt file) 27, 312
BC4078 BC4078 Acetoin transport permease protein (NCBI ptt file) 27, 312
BC4079 BC4079 Acetoin transport permease protein (NCBI ptt file) 27, 312
BC4249 BC4249 UDP-N-acetylglucosamine--N-acetylmuramyl-(Pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 27, 66
BC4285 BC4285 None 27, 133
BC4300 BC4300 hypothetical Metal-Binding Protein (NCBI ptt file) 27, 399
BC4301 BC4301 Metal-dependent phosphohydrolase (NCBI ptt file) 27, 399
BC4375 BC4375 Uridine kinase (NCBI ptt file) 49, 458
BC4376 BC4376 Protease (NCBI ptt file) 49, 458
BC4838 BC4838 ABC transporter permease protein (NCBI ptt file) 27, 312
BC5218 BC5218 Proton/sodium-glutamate symport protein (NCBI ptt file) 92, 458
BC5236 BC5236 Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file) 27, 75
BC5266 BC5266 Heteropolysaccharide repeat unit export protein (NCBI ptt file) 69, 458
BC5267 BC5267 Glycosyltransferase (NCBI ptt file) 69, 458
BC5268 BC5268 Secreted polysaccharide polymerase (NCBI ptt file) 69, 458
BC5269 BC5269 Amylovoran biosynthesis AmsK (NCBI ptt file) 69, 458
BC5270 BC5270 Undecaprenyl-phosphate galactosephosphotransferase (NCBI ptt file) 69, 458
BC5271 BC5271 UDP-N-acetylglucosamine 4-epimerase (NCBI ptt file) 69, 458
BC5272 BC5272 Carbamoyl-phosphate synthase small chain (NCBI ptt file) 69, 458
BC5273 BC5273 UDP-bacillosamine synthetase (NCBI ptt file) 69, 458
BC5455 BC5455 Sporulation kinase (NCBI ptt file) 143, 458
BC5456 BC5456 hypothetical Cytosolic Protein (NCBI ptt file) 143, 458
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 BC1290
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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