Organism : Bacillus cereus ATCC14579 | Module List :
BC1066

Signal transduction protein TRAP (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides cog/ cog
cytoplasm go/ cellular_component
oxidoreductase activity go/ molecular_function
antibiotic biosynthetic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1066
(Mouseover regulator name to see its description)

BC1066 is regulated by 28 influences and regulates 0 modules.
Regulators for BC1066 (28)
Regulator Module Operator
BC0123 233 tf
BC0586 233 tf
BC0613 233 tf
BC1710 233 tf
BC2166 233 tf
BC2794 233 tf
BC2801 233 tf
BC3405 233 tf
BC3668 233 tf
BC3706 233 tf
BC4001 233 tf
BC4029 233 tf
BC4072 233 tf
BC4670 233 tf
BC5200 233 tf
BC5205 233 tf
BC5332 233 tf
BC0123 173 tf
BC1080 173 tf
BC1710 173 tf
BC1915 173 tf
BC2672 173 tf
BC2738 173 tf
BC3814 173 tf
BC4072 173 tf
BC4652 173 tf
BC5197 173 tf
BC5481 173 tf

Warning: BC1066 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
4262 1.80e-03 AGGgGa
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4263 9.70e+03 CCTCCCG
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4382 7.00e-02 gaA.gGagGgg
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4383 1.20e+04 CGTacGGTGC
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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 BC1066

BC1066 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides cog/ cog
cytoplasm go/ cellular_component
oxidoreductase activity go/ molecular_function
antibiotic biosynthetic process go/ biological_process
Module neighborhood information for BC1066

BC1066 has total of 39 gene neighbors in modules 173, 233
Gene neighbors (39)
Gene Common Name Description Module membership
BC0237 BC0237 Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 98, 173
BC0387 BC0387 hypothetical protein (NCBI ptt file) 173, 211
BC0759 BC0759 Serine protease (NCBI ptt file) 233, 507
BC0868 BC0868 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 233, 507
BC1066 BC1066 Signal transduction protein TRAP (NCBI ptt file) 173, 233
BC1464 BC1464 hypothetical protein (NCBI ptt file) 173, 211
BC1467 BC1467 hypothetical protein (NCBI ptt file) 173, 211
BC1692 BC1692 hypothetical protein (NCBI ptt file) 173, 422
BC1717 BC1717 Peptidase E (NCBI ptt file) 173, 211
BC1803 BC1803 Manganese transport protein mntH (NCBI ptt file) 233, 287
BC1806 BC1806 2-dehydropantoate 2-reductase (NCBI ptt file) 107, 233
BC1947 BC1947 hypothetical protein (NCBI ptt file) 173, 420
BC2112 BC2112 None 173, 233
BC2114 BC2114 Glutathione peroxidase (NCBI ptt file) 48, 233
BC2292 BC2292 3-hydroxyisobutyryl-coenzyme A hydrolase (NCBI ptt file) 173, 203
BC2524 BC2524 Oligoendopeptidase F (NCBI ptt file) 173, 203
BC2533 BC2533 Methyltransferase (NCBI ptt file) 173, 211
BC2579 BC2579 hypothetical Cytosolic Protein (NCBI ptt file) 173, 211
BC2738 BC2738 Transcriptional regulator, AraC family (NCBI ptt file) 173, 203
BC3053 BC3053 HesB-like protein (NCBI ptt file) 233, 287
BC3054 BC3054 IG hypothetical 18636 (NCBI ptt file) 233, 287
BC3057 BC3057 Methyltransferase (NCBI ptt file) 173, 203
BC3453 BC3453 N-acyl homoserine lactone hydrolase (NCBI ptt file) 173, 180
BC3473 BC3473 Aminoglycoside N6'-acetyltransferase (NCBI ptt file) 173, 211
BC3478 BC3478 Phosphoglycerate mutase (NCBI ptt file) 233, 491
BC3483 BC3483 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 77, 233
BC3548 BC3548 Benzil reductase (NCBI ptt file) 233, 507
BC3672 BC3672 hypothetical protein (NCBI ptt file) 173, 409
BC3743 BC3743 Peptidase T (NCBI ptt file) 77, 233
BC4001 BC4001 Transcriptional repressor PadR (NCBI ptt file) 1, 233
BC4030 BC4030 D-beta-hydroxybutyrate dehydrogenase (NCBI ptt file) 173, 211
BC4092 BC4092 Stage II sporulation protein M (NCBI ptt file) 233, 511
BC4099 BC4099 hypothetical protein (NCBI ptt file) 233, 286
BC4144 BC4144 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 173, 211
BC4652 BC4652 Transcriptional regulator IcaR (NCBI ptt file) 173, 422
BC4691 BC4691 Thioredoxin (NCBI ptt file) 233, 507
BC5159 BC5159 Thioredoxin reductase (NCBI ptt file) 233, 507
BC5233 BC5233 D-alanine aminotransferase (NCBI ptt file) 233, 286
BC5322 BC5322 Nitrilotriacetate monooxygenase component B (NCBI ptt file) 173, 409
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 BC1066
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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