Organism : Bacillus cereus ATCC14579 | Module List :
BC3601

Two-component response regulator (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3601
(Mouseover regulator name to see its description)

BC3601 is regulated by 26 influences and regulates 0 modules.
Regulators for BC3601 (26)
Regulator Module Operator
BC0073 329 tf
BC0082 329 tf
BC0607 329 tf
BC1075 329 tf
BC1427 329 tf
BC1489 329 tf
BC1814 329 tf
BC1819 329 tf
BC2351 329 tf
BC3356 329 tf
BC3982 329 tf
BC4010 329 tf
BC4374 329 tf
BC5200 329 tf
BC5411 329 tf
BC0840 64 tf
BC0880 64 tf
BC1329 64 tf
BC1719 64 tf
BC3095 64 tf
BC3756 64 tf
BC4091 64 tf
BC4204 64 tf
BC4499 64 tf
BC5010 64 tf
BC5339 64 tf

Warning: BC3601 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
4048 9.80e+02 TccTTCTATg
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4049 6.60e+03 cggTagAgcAgcAttTagcg
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4572 2.00e+00 AagtAgaAgAAGgG.atg
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4573 5.00e+00 AaaGaGGaaA.aG
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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 BC3601

BC3601 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC3601

BC3601 has total of 33 gene neighbors in modules 64, 329
Gene neighbors (33)
Gene Common Name Description Module membership
BC0036 BC0036 Thymidylate kinase (NCBI ptt file) 230, 329
BC0039 BC0039 hypothetical protein (NCBI ptt file) 64, 403
BC0073 BC0073 Bvg accessory factor (NCBI ptt file) 240, 329
BC0206 BC0206 hypothetical protein (NCBI ptt file) 64, 431
BC0262 BC0262 Holo-[acyl-carrier protein] synthase (NCBI ptt file) 177, 329
BC0609 BC0609 Lactoylglutathione lyase (NCBI ptt file) 252, 329
BC0700 BC0700 hypothetical protein (NCBI ptt file) 64, 433
BC0834 BC0834 hypothetical protein (NCBI ptt file) 64, 265
BC1035 BC1035 Glycerol kinase (NCBI ptt file) 252, 329
BC1036 BC1036 Glycerol-3-phosphate dehydrogenase (NCBI ptt file) 18, 329
BC1283 BC1283 SinI protein (NCBI ptt file) 64, 354
BC1300 BC1300 Two-component response regulator (NCBI ptt file) 252, 329
BC1301 BC1301 Two component system histidine kinase (NCBI ptt file) 252, 329
BC1416 BC1416 CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 64, 219
BC1525 BC1525 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 88
BC1526 BC1526 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 300
BC1540 BC1540 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI ptt file) 329, 450
BC1541 BC1541 Pantoate--beta-alanine ligase (NCBI ptt file) 329, 450
BC1542 BC1542 Aspartate 1-decarboxylase (NCBI ptt file) 329, 450
BC1672 BC1672 Metal-dependent hydrolase related to alanyl-tRNA synthetase (NCBI ptt file) 141, 329
BC1682 BC1682 hypothetical protein (NCBI ptt file) 64, 461
BC1814 BC1814 Transcriptional regulator, TetR family (NCBI ptt file) 329, 386
BC2036 BC2036 hypothetical Membrane Spanning Protein (NCBI ptt file) 159, 329
BC2037 BC2037 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 329
BC2890 BC2890 hypothetical protein (NCBI ptt file) 64, 118
BC3601 BC3601 Two-component response regulator (NCBI ptt file) 64, 329
BC3713 BC3713 Hfq protein (NCBI ptt file) 64, 354
BC4481 BC4481 TPR repeat protein (NCBI ptt file) 329, 385
BC4489 BC4489 hypothetical Cytosolic Protein (NCBI ptt file) 64, 274
BC4796 BC4796 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 126
BC4850 BC4850 None 329, 451
BC5384 BC5384 hypothetical Cytosolic Protein (NCBI ptt file) 37, 64
BC5479 BC5479 Mechanosensitive ion channel (NCBI ptt file) 88, 329
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 BC3601
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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