Organism : Bacillus cereus ATCC14579 | Module List :
BC0384

hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0384
(Mouseover regulator name to see its description)

BC0384 is regulated by 19 influences and regulates 0 modules.
Regulators for BC0384 (19)
Regulator Module Operator
BC0230 48 tf
BC0499 48 tf
BC1080 48 tf
BC2218 48 tf
BC2410 48 tf
BC2770 48 tf
BC3706 48 tf
BC4072 48 tf
BC4499 48 tf
BC4652 48 tf
BC5024 48 tf
BC0742 504 tf
BC2410 504 tf
BC3253 504 tf
BC3903 504 tf
BC4499 504 tf
BC5173 504 tf
BC5200 504 tf
BC5205 504 tf

Warning: BC0384 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
4016 2.00e-06 aGAGGgGagA
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4017 5.10e+03 GaAcTTTCTGTtg
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4918 8.90e+02 agaggGGG
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4919 7.10e+00 CATaTAcgcTAAaatAGaAgAA
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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 BC0384

Warning: No Functional annotations were found!

Module neighborhood information for BC0384

BC0384 has total of 39 gene neighbors in modules 48, 504
Gene neighbors (39)
Gene Common Name Description Module membership
BC0318 BC0318 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 48, 241
BC0384 BC0384 hypothetical protein (NCBI ptt file) 48, 504
BC0385 BC0385 Thioredoxin reductase (NCBI ptt file) 48, 335
BC0499 BC0499 Transcriptional regulator (NCBI ptt file) 48, 475
BC0571 BC0571 Serine/threonine protein phosphatase (NCBI ptt file) 48, 497
BC0589 BC0589 Formate dehydrogenase alpha chain (NCBI ptt file) 48, 475
BC0590 BC0590 hypothetical protein (NCBI ptt file) 48, 218
BC1085 BC1085 Metal-dependent hydrolase (NCBI ptt file) 48, 127
BC1088 BC1088 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 317, 504
BC1153 BC1153 Asparagine synthetase (NCBI ptt file) 397, 504
BC1449 BC1449 cAMP-dependent protein kinase regulatory chain (NCBI ptt file) 217, 504
BC1450 BC1450 hypothetical protein (NCBI ptt file) 241, 504
BC1524 BC1524 Menaquinol-cytochrome c reductase cytochrome c subunit (NCBI ptt file) 48, 150
BC1931 BC1931 Branched-chain amino acid transport system permease protein livM (NCBI ptt file) 48, 449
BC1978 BC1978 Siderophore biosynthesis protein (NCBI ptt file) 46, 504
BC1982 BC1982 hypothetical protein (NCBI ptt file) 504, 520
BC1983 BC1983 hypothetical Cytosolic Protein (NCBI ptt file) 46, 504
BC2043 BC2043 IG hypothetical 17883 (NCBI ptt file) 303, 504
BC2066 BC2066 Macrolide glycosyltransferase (NCBI ptt file) 48, 496
BC2113 BC2113 hypothetical protein (NCBI ptt file) 48, 496
BC2114 BC2114 Glutathione peroxidase (NCBI ptt file) 48, 233
BC2239 BC2239 hypothetical protein (NCBI ptt file) 26, 504
BC2559 BC2559 Phage protein (NCBI ptt file) 184, 504
BC2732 BC2732 hypothetical protein (NCBI ptt file) 48, 491
BC2790 BC2790 Glycine betaine transport system permease protein (NCBI ptt file) 397, 504
BC2969 BC2969 hypothetical protein (NCBI ptt file) 48, 77
BC3191 BC3191 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 125, 504
BC3443 BC3443 hypothetical Membrane Spanning Protein (NCBI ptt file) 48, 491
BC3488 BC3488 hypothetical Membrane Spanning Protein (NCBI ptt file) 502, 504
BC3489 BC3489 Agmatine deiminase (NCBI ptt file) 502, 504
BC4464 BC4464 Folylpolyglutamate synthase (NCBI ptt file) 48, 63
BC4529 BC4529 None 184, 504
BC4623 BC4623 Alanine dehydrogenase (NCBI ptt file) 48, 194
BC4784 BC4784 hypothetical protein (NCBI ptt file) 199, 504
BC5022 BC5022 Cytolysin immunity CylI (NCBI ptt file) 48, 484
BC5023 BC5023 hypothetical protein (NCBI ptt file) 48, 484
BC5024 BC5024 Transcriptional regulator, PBSX family (NCBI ptt file) 48, 484
BC5036 BC5036 Bacillolysin (NCBI ptt file) 209, 504
BC5173 BC5173 Transcriptional regulator, PBSX family (NCBI ptt file) 184, 504
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 BC0384
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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