Organism : Bacillus cereus ATCC14579 | Module List :
BC0586

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 BC0586
(Mouseover regulator name to see its description)

BC0586 is regulated by 20 influences and regulates 28 modules.
Regulators for BC0586 (20)
Regulator Module Operator
BC0586 268 tf
BC1302 268 tf
BC1489 268 tf
BC1490 268 tf
BC1531 268 tf
BC4570 268 tf
BC5352 268 tf
BC0057 527 tf
BC0114 527 tf
BC0586 527 tf
BC1302 527 tf
BC1489 527 tf
BC1490 527 tf
BC1531 527 tf
BC3668 527 tf
BC4316 527 tf
BC4589 527 tf
BC4603 527 tf
BC4672 527 tf
BC5339 527 tf

Warning: BC0586 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
4452 1.40e+02 gaagcgagtGTaG
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4453 1.20e+02 AGGGGa
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4964 4.00e-02 cC.CtcccTTc
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4965 3.20e+01 GagggGggtgc
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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 BC0586

BC0586 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC0586

BC0586 has total of 40 gene neighbors in modules 268, 527
Gene neighbors (40)
Gene Common Name Description Module membership
BC0103 BC0103 DNA repair protein RadA (NCBI ptt file) 483, 527
BC0104 BC0104 DNA-binding protein (NCBI ptt file) 483, 527
BC0514 BC0514 Daunorubicin resistance transmembrane protein (NCBI ptt file) 467, 527
BC0585 BC0585 Two component system histidine kinase (NCBI ptt file) 268, 527
BC0586 BC0586 Two-component response regulator (NCBI ptt file) 268, 527
BC0804 BC0804 Quinolone resistence NorA protein (NCBI ptt file) 268, 439
BC0939 BC0939 Type II restriction-modification system restriction subunit (NCBI ptt file) 98, 527
BC0940 BC0940 Type II restriction-modification system restriction subunit (NCBI ptt file) 98, 527
BC1135 BC1135 Alkaline phosphatase like protein (NCBI ptt file) 268, 439
BC1184 BC1184 Na+ driven multidrug efflux pump (NCBI ptt file) 243, 527
BC1190 BC1190 genetic competence negative regulator mecA (NCBI ptt file) 268, 438
BC1191 BC1191 Cardiolipin synthetase (NCBI ptt file) 268, 527
BC1307 BC1307 hypothetical protein (NCBI ptt file) 511, 527
BC1485 BC1485 ATP-dependent DNA helicase recQ (NCBI ptt file) 268, 450
BC1486 BC1486 CAAX amino terminal protease family (NCBI ptt file) 268, 450
BC1488 BC1488 phosphoesterase (NCBI ptt file) 268, 450
BC1489 BC1489 Transcriptional regulator, MerR family (NCBI ptt file) 268, 450
BC1490 BC1490 genetic competence negative regulator mecA (NCBI ptt file) 268, 439
BC1520 BC1520 hypothetical Cytosolic Protein (NCBI ptt file) 208, 268
BC1532 BC1532 Dihydrodipicolinate reductase (NCBI ptt file) 450, 527
BC2405 BC2405 hypothetical protein (NCBI ptt file) 268, 439
BC3461 BC3461 LMBE-related protein (NCBI ptt file) 152, 268
BC3462 BC3462 hypothetical protein (NCBI ptt file) 268, 306
BC3559 BC3559 Chloramphenicol-sensitive protein rarD (NCBI ptt file) 208, 527
BC3920 BC3920 2-dehydropantoate 2-reductase (NCBI ptt file) 268, 450
BC3958 BC3958 Myo-inositol-1(or 4)-monophosphatase (NCBI ptt file) 122, 527
BC3979 BC3979 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 117, 527
BC4098 BC4098 Glutamate-rich protein grpB (NCBI ptt file) 268, 511
BC4316 BC4316 Transcriptional regulator, MarR family (NCBI ptt file) 390, 527
BC4477 BC4477 ATP-dependent protease La (NCBI ptt file) 99, 527
BC4570 BC4570 Transcriptional regulator, TetR family (NCBI ptt file) 268, 507
BC4588 BC4588 Phosphate regulon sensor protein phoR (NCBI ptt file) 261, 527
BC4589 BC4589 Alkaline phosphatase synthesis two-component response regulator phoP (NCBI ptt file) 41, 527
BC4605 BC4605 DNA polymerase III alpha subunit (NCBI ptt file) 268, 450
BC4608 BC4608 phosphoesterase, DHH family protein (NCBI ptt file) 268, 439
BC4689 BC4689 tRNA binding domain protein (NCBI ptt file) 270, 527
BC4690 BC4690 hypothetical Cytosolic Protein (NCBI ptt file) 270, 527
BC4707 BC4707 Multidrug resistance protein B (NCBI ptt file) 79, 527
BC5107 BC5107 Two-component response regulator (NCBI ptt file) 268, 505
BC5426 BC5426 Acyl-CoA hydrolase (NCBI ptt file) 268, 527
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 BC0586
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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