Organism : Bacillus cereus ATCC14579 | Module List :
BC0572

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 BC0572
(Mouseover regulator name to see its description)

BC0572 is regulated by 19 influences and regulates 0 modules.
Regulators for BC0572 (19)
Regulator Module Operator
BC0123 286 tf
BC0758 286 tf
BC1449 286 tf
BC1996 286 tf
BC2794 286 tf
BC3072 286 tf
BC3668 286 tf
BC4001 286 tf
BC5265 286 tf
BC5352 286 tf
BC0649 63 tf
BC0758 63 tf
BC0950 63 tf
BC2444 63 tf
BC2794 63 tf
BC3160 63 tf
BC3244 63 tf
BC3493 63 tf
BC3497 63 tf

Warning: BC0572 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
4046 1.20e+04 GaGgaggA
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4047 1.90e+04 CAGCGCCc
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4488 1.20e+00 aAGGAgatGa
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4489 1.90e+04 ggGaAtAGGga
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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 BC0572

BC0572 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC0572

BC0572 has total of 62 gene neighbors in modules 63, 286
Gene neighbors (62)
Gene Common Name Description Module membership
BC0013 BC0013 Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) 63, 137
BC0565 BC0565 Ankyrin (NCBI ptt file) 63, 265
BC0572 BC0572 Two-component response regulator (NCBI ptt file) 63, 286
BC0649 BC0649 Transcriptional regulator, DeoR family (NCBI ptt file) 63, 246
BC0758 BC0758 Transcriptional regulator, MarR family (NCBI ptt file) 47, 286
BC0761 BC0761 ABC transporter permease protein (NCBI ptt file) 286, 427
BC0762 BC0762 hypothetical protein (NCBI ptt file) 286, 427
BC0763 BC0763 ABC transporter permease protein (NCBI ptt file) 286, 427
BC0766 BC0766 Methylthioribose transport system permease protein (NCBI ptt file) 20, 63
BC1097 BC1097 hypothetical protein (NCBI ptt file) 63, 286
BC1098 BC1098 hypothetical protein (NCBI ptt file) 286, 427
BC1099 BC1099 hypothetical protein (NCBI ptt file) 26, 286
BC1258 BC1258 hypothetical protein (NCBI ptt file) 63, 427
BC1269 BC1269 hypothetical protein (NCBI ptt file) 286, 427
BC1275 BC1275 Methyltransferase (NCBI ptt file) 47, 286
BC1484 BC1484 ATP-dependent DNA helicase recQ (NCBI ptt file) 286, 409
BC1519 BC1519 TPR-repeat-containing protein (NCBI ptt file) 286, 306
BC1588 BC1588 Secreted polysaccharide polymerase (NCBI ptt file) 286, 427
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1912 BC1912 Phage protein (NCBI ptt file) 63, 137
BC1913 BC1913 Phage protein (NCBI ptt file) 63, 137
BC1914 BC1914 Phage protein (NCBI ptt file) 63, 146
BC2315 BC2315 DinB protein (NCBI ptt file) 63, 163
BC2407 BC2407 hypothetical protein (NCBI ptt file) 286, 453
BC2428 BC2428 hypothetical protein (NCBI ptt file) 63, 225
BC2539 BC2539 Two-component sensor kinase yxdK (NCBI ptt file) 6, 63
BC2556 BC2556 DNA integration/recombination/invertion protein (NCBI ptt file) 286, 511
BC2603 BC2603 hypothetical protein (NCBI ptt file) 63, 299
BC2740 BC2740 Protein translocase subunit SecY (NCBI ptt file) 6, 63
BC2794 BC2794 RNA polymerase ECF-type sigma factor (NCBI ptt file) 63, 105
BC3026 BC3026 Tetracycline resistance protein tetP (NCBI ptt file) 286, 511
BC3107 BC3107 UvrC-like protein (NCBI ptt file) 286, 491
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3484 BC3484 Oligoendopeptidase F (NCBI ptt file) 286, 439
BC3497 BC3497 Transcriptional regulator, ArsR family (NCBI ptt file) 63, 146
BC3498 BC3498 Quinone oxidoreductase (NCBI ptt file) 63, 465
BC3584 BC3584 Oligopeptide-binding protein oppA (NCBI ptt file) 55, 63
BC3645 BC3645 CcdC protein (NCBI ptt file) 63, 285
BC3727 BC3727 Formate transporter (NCBI ptt file) 47, 286
BC3747 BC3747 Sensory box/GGDEF family protein (NCBI ptt file) 63, 286
BC3876 BC3876 hypothetical protein (NCBI ptt file) 63, 228
BC4014 BC4014 Neopullulanase (NCBI ptt file) 63, 299
BC4099 BC4099 hypothetical protein (NCBI ptt file) 233, 286
BC4131 BC4131 hypothetical protein (NCBI ptt file) 63, 299
BC4146 BC4146 Protein erfK/srfK precursor (NCBI ptt file) 20, 63
BC4147 BC4147 Integral membrane protein (NCBI ptt file) 63, 482
BC4305 BC4305 hypothetical Cytosolic Protein (NCBI ptt file) 63, 72
BC4340 BC4340 NAD(P)H nitroreductase (NCBI ptt file) 47, 286
BC4464 BC4464 Folylpolyglutamate synthase (NCBI ptt file) 48, 63
BC4514 BC4514 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 63, 288
BC4666 BC4666 Two component system histidine kinase (NCBI ptt file) 63, 308
BC4674 BC4674 Chorismate mutase (NCBI ptt file) 286, 288
BC4729 BC4729 hypothetical protein (NCBI ptt file) 286, 427
BC4730 BC4730 Homoserine O-acetyltransferase (NCBI ptt file) 286, 398
BC4839 BC4839 ABC transporter ATP-binding protein (NCBI ptt file) 63, 453
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
BC4947 BC4947 hypothetical protein (NCBI ptt file) 20, 63
BC5068 BC5068 CrcB family protein (NCBI ptt file) 63, 285
BC5233 BC5233 D-alanine aminotransferase (NCBI ptt file) 233, 286
BC5400 BC5400 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 237, 286
BC5441 BC5441 Autolysin sensor kinase (NCBI ptt file) 286, 414
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 BC0572
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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