Organism : Bacillus cereus ATCC14579 | Module List :
BC2217

Two-component response regulator yhcZ (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2217
(Mouseover regulator name to see its description)

BC2217 is regulated by 24 influences and regulates 14 modules.
Regulators for BC2217 (24)
Regulator Module Operator
BC0123 279 tf
BC0224 279 tf
BC0356 279 tf
BC0953 279 tf
BC1698 279 tf
BC2217 279 tf
BC2526 279 tf
BC2738 279 tf
BC2914 279 tf
BC3449 279 tf
BC3493 279 tf
BC3589 279 tf
BC4212 279 tf
BC4277 279 tf
BC4960 279 tf
BC0954 218 tf
BC1032 218 tf
BC1427 218 tf
BC1490 218 tf
BC2632 218 tf
BC2979 218 tf
BC3493 218 tf
BC4010 218 tf
BC5097 218 tf

Warning: BC2217 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
4352 9.70e-05 agagaGG.Gata.aa
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4353 2.00e+04 CCATCGcccCTTGC
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4474 7.60e-01 AaaAtagGggg
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4475 5.50e+03 AgaagAAatGg
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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 BC2217

BC2217 is enriched for 7 functions in 3 categories.
Module neighborhood information for BC2217

BC2217 has total of 67 gene neighbors in modules 218, 279
Gene neighbors (67)
Gene Common Name Description Module membership
BC0356 BC0356 Sigma-54-dependent transcriptional activator (NCBI ptt file) 279, 525
BC0374 BC0374 Amidohydrolase amhX (NCBI ptt file) 139, 218
BC0398 BC0398 Benzoate transport protein (NCBI ptt file) 76, 218
BC0582 BC0582 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 218
BC0590 BC0590 hypothetical protein (NCBI ptt file) 48, 218
BC0827 BC0827 hypothetical protein (NCBI ptt file) 141, 218
BC0829 BC0829 hypothetical protein (NCBI ptt file) 86, 218
BC0890 BC0890 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 146, 279
BC0899 BC0899 hypothetical protein (NCBI ptt file) 85, 279
BC0919 BC0919 hypothetical protein (NCBI ptt file) 279, 425
BC0929 BC0929 hypothetical protein (NCBI ptt file) 85, 279
BC0930 BC0930 hypothetical protein (NCBI ptt file) 248, 279
BC0931 BC0931 hypothetical Membrane Spanning Protein (NCBI ptt file) 248, 279
BC0944 BC0944 hypothetical protein (NCBI ptt file) 85, 279
BC1127 BC1127 Malate synthase (NCBI ptt file) 163, 218
BC1128 BC1128 Isocitrate lyase (NCBI ptt file) 218, 400
BC1202 BC1202 Serine/threonine protein phosphatase (NCBI ptt file) 72, 218
BC1253 BC1253 Transcriptional regulator, PBSX family (NCBI ptt file) 279, 316
BC1340 BC1340 Sporulation kinase (NCBI ptt file) 218, 434
BC1675 BC1675 Branched-chain amino acid transport protein azlD (NCBI ptt file) 218, 416
BC1801 BC1801 Sensor protein vanS (NCBI ptt file) 212, 279
BC2013 BC2013 Alpha/beta hydrolase (NCBI ptt file) 52, 218
BC2042 BC2042 putative NAD-dependent dehydrogenase (NCBI ptt file) 218, 243
BC2216 BC2216 Two-component sensor protein yhcY (NCBI ptt file) 279, 424
BC2217 BC2217 Two-component response regulator yhcZ (NCBI ptt file) 218, 279
BC2281 BC2281 Multimodular transpeptidase-transglycosylase PBP 1A (NCBI ptt file) 218, 375
BC2286 BC2286 2-methylisocitrate dehydratase (NCBI ptt file) 279, 355
BC2288 BC2288 Acyl-CoA dehydrogenase (NCBI ptt file) 212, 279
BC2395 BC2395 hypothetical protein (NCBI ptt file) 218, 321
BC2663 BC2663 None 218, 225
BC2708 BC2708 hypothetical Cytosolic Protein (NCBI ptt file) 279, 395
BC2709 BC2709 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 163, 279
BC2750 BC2750 hypothetical protein (NCBI ptt file) 20, 279
BC2757 BC2757 Tryptophan 2,3-dioxygenase (NCBI ptt file) 137, 218
BC2759 BC2759 L-kynurenine hydrolase (NCBI ptt file) 137, 218
BC2838 BC2838 hypothetical protein (NCBI ptt file) 76, 218
BC2869 BC2869 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file) 279, 524
BC2899 BC2899 2'-5' RNA ligase (NCBI ptt file) 52, 218
BC3022 BC3022 hypothetical protein (NCBI ptt file) 127, 218
BC3124 BC3124 Isochorismatase family (NCBI ptt file) 218, 313
BC3162 BC3162 Bicyclomycin resistance protein (NCBI ptt file) 150, 218
BC3231 BC3231 Microcin C7 self-immunity protein mccF (NCBI ptt file) 279, 409
BC3248 BC3248 D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 218, 359
BC3261 BC3261 hypothetical protein (NCBI ptt file) 30, 279
BC3594 BC3594 PhnB protein (NCBI ptt file) 141, 218
BC3634 BC3634 Acetyltransferase (NCBI ptt file) 212, 279
BC3656 BC3656 Methyltransferase (NCBI ptt file) 218, 303
BC3657 BC3657 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (NCBI ptt file) 218, 359
BC3694 BC3694 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 30, 279
BC3695 BC3695 holin (NCBI ptt file) 30, 279
BC3696 BC3696 XpaF1 protein (NCBI ptt file) 279, 424
BC3698 BC3698 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 30, 279
BC3699 BC3699 Antigen (NCBI ptt file) 30, 279
BC3939 BC3939 Amidase (NCBI ptt file) 218, 461
BC3993 BC3993 Polyphosphate kinase (NCBI ptt file) 57, 218
BC4003 BC4003 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file) 194, 218
BC4042 BC4042 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) 193, 218
BC4043 BC4043 Penicillin-binding protein (NCBI ptt file) 279, 469
BC4082 BC4082 hypothetical protein (NCBI ptt file) 218, 361
BC4223 BC4223 hypothetical protein (NCBI ptt file) 72, 279
BC4234 BC4234 ComG operon protein 7 (NCBI ptt file) 279, 359
BC4598 BC4598 FxsA protein (NCBI ptt file) 31, 218
BC4621 BC4621 hypothetical protein (NCBI ptt file) 279, 316
BC4668 BC4668 Virulence factor mviM (NCBI ptt file) 125, 218
BC4767 BC4767 hypothetical protein (NCBI ptt file) 218, 405
BC4824 BC4824 ABC transporter ATP-binding protein (NCBI ptt file) 2, 279
BC5366 BC5366 Muramoyltetrapeptide carboxypeptidase (NCBI ptt file) 139, 218
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 BC2217
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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