Organism : Bacillus cereus ATCC14579 | Module List :
BC4589

Alkaline phosphatase synthesis two-component response regulator phoP (NCBI ptt file)

CircVis
Functional Annotations (9)
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
carboxy-lyase activity go/ molecular_function
carboxylic acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4589
(Mouseover regulator name to see its description)

BC4589 is regulated by 27 influences and regulates 10 modules.
Regulators for BC4589 (27)
Regulator Module Operator
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
BC0840 41 tf
BC1329 41 tf
BC1710 41 tf
BC1715 41 tf
BC1719 41 tf
BC2178 41 tf
BC2815 41 tf
BC3668 41 tf
BC3976 41 tf
BC4505 41 tf
BC4589 41 tf
BC4930 41 tf
BC5010 41 tf
BC5352 41 tf

Warning: BC4589 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
4002 2.50e-02 tttcccTTTct
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4003 2.10e+03 cCcGGGGC
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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 BC4589

BC4589 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
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
carboxy-lyase activity go/ molecular_function
carboxylic acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Two-component system kegg/ kegg pathway
Module neighborhood information for BC4589

BC4589 has total of 43 gene neighbors in modules 41, 527
Gene neighbors (43)
Gene Common Name Description Module membership
BC0065 BC0065 Cell division protein DIVIC (NCBI ptt file) 41, 275
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
BC0539 BC0539 hypothetical protein (RefSeq) 41, 169
BC0585 BC0585 Two component system histidine kinase (NCBI ptt file) 268, 527
BC0586 BC0586 Two-component response regulator (NCBI ptt file) 268, 527
BC0840 BC0840 Transcriptional regulator, RpiR family (NCBI ptt file) 41, 261
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
BC1023 BC1023 Transporter, LysE family (NCBI ptt file) 41, 480
BC1184 BC1184 Na+ driven multidrug efflux pump (NCBI ptt file) 243, 527
BC1191 BC1191 Cardiolipin synthetase (NCBI ptt file) 268, 527
BC1298 BC1298 Carbohydrate diacid regulator (NCBI ptt file) 41, 261
BC1307 BC1307 hypothetical protein (NCBI ptt file) 511, 527
BC1532 BC1532 Dihydrodipicolinate reductase (NCBI ptt file) 450, 527
BC1744 BC1744 SWF/SNF family helicase (NCBI ptt file) 41, 406
BC1934 BC1934 hypothetical protein (NCBI ptt file) 41, 180
BC2295 BC2295 Exonuclease SbcD (NCBI ptt file) 41, 193
BC2447 BC2447 Chloramphenicol acetyltransferase (NCBI ptt file) 41, 98
BC2748 BC2748 Integral membrane protein (NCBI ptt file) 41, 228
BC2886 BC2886 hypothetical protein (NCBI ptt file) 41, 354
BC3559 BC3559 Chloramphenicol-sensitive protein rarD (NCBI ptt file) 208, 527
BC3611 BC3611 DNA polymerase III alpha subunit (NCBI ptt file) 41, 261
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
BC4262 BC4262 5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file) 41, 394
BC4316 BC4316 Transcriptional regulator, MarR family (NCBI ptt file) 390, 527
BC4321 BC4321 DNA polymerase III, delta subunit (NCBI ptt file) 41, 273
BC4477 BC4477 ATP-dependent protease La (NCBI ptt file) 99, 527
BC4505 BC4505 Transcriptional regulator (NCBI ptt file) 41, 261
BC4562 BC4562 23S rRNA methyltransferase (NCBI ptt file) 41, 261
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
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
BC4727 BC4727 hypothetical protein (NCBI ptt file) 41, 385
BC4728 BC4728 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 41, 90
BC5028 BC5028 Two-component response regulator vanRB (NCBI ptt file) 6, 41
BC5352 BC5352 two-component response regulator YocG (NCBI) 41, 440
BC5353 BC5353 Two-component sensor kinase yocF (NCBI ptt file) 41, 440
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 BC4589
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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