Organism : Bacillus cereus ATCC14579 | Module List :
BC2839

Sarcosine oxidase alpha subunit (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
electron transport go/ biological_process
sarcosine oxidase activity go/ molecular_function
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2839
(Mouseover regulator name to see its description)

BC2839 is regulated by 21 influences and regulates 0 modules.
Regulators for BC2839 (21)
Regulator Module Operator
BC0659 524 tf
BC2549 524 tf
BC2837 524 tf
BC3069 524 tf
BC3704 524 tf
BC4212 524 tf
BC4256 524 tf
BC4474 524 tf
BC4570 524 tf
BC4650 524 tf
BC0785 267 tf
BC1329 267 tf
BC2410 267 tf
BC2469 267 tf
BC2517 267 tf
BC3025 267 tf
BC3587 267 tf
BC3588 267 tf
BC4960 267 tf
BC5251 267 tf
BC5282 267 tf

Warning: BC2839 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
4450 7.50e+01 TtTTgaggtG
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4451 3.30e+03 ccTcCtt
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4958 3.50e-03 AAGGGG
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4959 7.00e+03 GcGGCaaGCG
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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 BC2839

BC2839 is enriched for 6 functions in 4 categories.
Enrichment Table (6)
Function System
electron transport go/ biological_process
sarcosine oxidase activity go/ molecular_function
electron carrier activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BC2839

BC2839 has total of 33 gene neighbors in modules 267, 524
Gene neighbors (33)
Gene Common Name Description Module membership
BC0192 BC0192 Acylamino-acid-releasing enzyme (NCBI ptt file) 375, 524
BC0326 BC0326 phosphoribosylaminoimidazole-succinocarboxamidesynthase (RefSeq) 424, 524
BC0327 BC0327 Phosphorybosylformylglycinamidine synthetase, PurS component (NCBI ptt file) 72, 524
BC0328 BC0328 Phosphoribosylformylglycinamidine synthase (NCBI ptt file) 72, 524
BC0329 BC0329 Phosphoribosylformylglycinamidine synthase (NCBI ptt file) 424, 524
BC0331 BC0331 Phosphoribosylformylglycinamidine cyclo-ligase (NCBI ptt file) 424, 524
BC0332 BC0332 Phosphoribosylglycinamide formyltransferase (NCBI ptt file) 424, 524
BC0650 BC0650 Pyrimidine Reductase (NCBI ptt file) 248, 267
BC0653 BC0653 hypothetical Cytosolic Protein (NCBI ptt file) 162, 267
BC0659 BC0659 Ribose operon repressor (NCBI ptt file) 417, 524
BC0660 BC0660 Ribokinase (NCBI ptt file) 417, 524
BC0661 BC0661 High affinity ribose transport protein rbsD (NCBI ptt file) 417, 524
BC0662 BC0662 Ribose transport ATP-binding protein rbsA (NCBI ptt file) 417, 524
BC0918 BC0918 IG hypothetical 23633 (NCBI ptt file) 401, 524
BC1019 BC1019 phosphoesterase (NCBI ptt file) 50, 524
BC1517 BC1517 3-dehydroquinate synthase (NCBI ptt file) 83, 524
BC1522 BC1522 Menaquinol-cytochrome c reductase iron-sulfur subunit (NCBI ptt file) 83, 524
BC1795 BC1795 hypothetical protein (NCBI ptt file) 460, 524
BC2129 BC2129 hypothetical protein (NCBI ptt file) 80, 267
BC2336 BC2336 hypothetical Membrane Spanning Protein (NCBI ptt file) 115, 267
BC2397 BC2397 ATPase family protein (NCBI ptt file) 437, 524
BC2839 BC2839 Sarcosine oxidase alpha subunit (NCBI ptt file) 267, 524
BC2840 BC2840 Sarcosine oxidase alpha subunit (NCBI ptt file) 106, 267
BC2869 BC2869 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file) 279, 524
BC3208 BC3208 hypothetical protein (NCBI ptt file) 220, 267
BC3433 BC3433 hypothetical protein (NCBI ptt file) 267, 454
BC3564 BC3564 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 153, 267
BC4065 BC4065 Stage V sporulation protein AE (NCBI ptt file) 355, 524
BC4069 BC4069 Stage V sporulation protein AB (NCBI ptt file) 424, 524
BC4487 BC4487 Superfamily I DNA and RNA helicases (NCBI ptt file) 518, 524
BC4974 BC4974 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 84, 267
BC5246 BC5246 hypothetical protein (NCBI ptt file) 125, 267
BC5334 BC5334 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI ptt file) 54, 524
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 BC2839
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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