Organism : Bacillus cereus ATCC14579 | Module List :
BC0577

Two-component sensor kinase yufL (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Signal transduction histidine kinase regulating citrate/malate metabolism cog/ cog
protein histidine kinase activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
peptidyl-histidine phosphorylation go/ biological_process
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0577
(Mouseover regulator name to see its description)

BC0577 is regulated by 23 influences and regulates 0 modules.
Regulators for BC0577 (23)
Regulator Module Operator
BC0518 462 tf
BC0613 462 tf
BC0648 462 tf
BC1302 462 tf
BC1622 462 tf
BC2166 462 tf
BC2218 462 tf
BC2434 462 tf
BC2526 462 tf
BC2672 462 tf
BC3025 462 tf
BC3072 462 tf
BC3814 462 tf
BC3961 462 tf
BC4525 462 tf
BC4650 462 tf
BC4703 462 tf
BC0648 50 tf
BC2742 50 tf
BC4211 50 tf
BC4650 50 tf
BC4703 50 tf
BC5481 50 tf

Warning: BC0577 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
4020 7.70e-04 AGGAgG
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4021 4.00e+04 CAGccAG
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4834 4.00e-05 AaGGagGa
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4835 4.70e+01 tcTctTTttgt
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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 BC0577

BC0577 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Signal transduction histidine kinase regulating citrate/malate metabolism cog/ cog
protein histidine kinase activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
peptidyl-histidine phosphorylation go/ biological_process
Two-component system kegg/ kegg pathway
Module neighborhood information for BC0577

BC0577 has total of 55 gene neighbors in modules 50, 462
Gene neighbors (55)
Gene Common Name Description Module membership
BC0163 BC0163 tRNA pseudouridine synthase A (NCBI ptt file) 157, 462
BC0166 BC0166 hypothetical Cytosolic Protein (NCBI ptt file) 76, 462
BC0167 BC0167 Spore-specific N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 76, 462
BC0201 BC0201 L-gulonolactone oxidase (NCBI ptt file) 461, 462
BC0202 BC0202 Multidrug resistance protein B (NCBI ptt file) 461, 462
BC0225 BC0225 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 410, 462
BC0422 BC0422 Methyl-accepting chemotaxis protein (NCBI ptt file) 213, 462
BC0423 BC0423 Peptide synthetase (NCBI ptt file) 213, 462
BC0576 BC0576 Methyl-accepting chemotaxis protein (NCBI ptt file) 2, 462
BC0577 BC0577 Two-component sensor kinase yufL (NCBI ptt file) 50, 462
BC0648 BC0648 ECF-type sigma factor negative effector (NCBI ptt file) 50, 60
BC0887 BC0887 Collagen adhesion protein (NCBI ptt file) 341, 462
BC0896 BC0896 S-layer protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (NCBI ptt file) 50, 492
BC0943 BC0943 hypothetical protein (NCBI ptt file) 50, 492
BC1019 BC1019 phosphoesterase (NCBI ptt file) 50, 524
BC1629 BC1629 Chemotaxis protein cheC (NCBI ptt file) 50, 83
BC1630 BC1630 hypothetical protein (NCBI ptt file) 50, 83
BC1631 BC1631 hypothetical protein (NCBI ptt file) 50, 76
BC1635 BC1635 hypothetical protein (NCBI ptt file) 50, 492
BC1636 BC1636 Flagellar hook-associated protein 1 (NCBI ptt file) 50, 492
BC1637 BC1637 Flagellar hook-associated protein 3 (NCBI ptt file) 50, 492
BC1638 BC1638 Flagellar hook-associated protein 2 (NCBI ptt file) 50, 492
BC1641 BC1641 Flagellar basal-body rod protein flgB (NCBI ptt file) 50, 492
BC1642 BC1642 Flagellar basal-body rod protein flgC (NCBI ptt file) 50, 492
BC1643 BC1643 Flagellar hook-basal body complex protein fliE (NCBI ptt file) 50, 492
BC1644 BC1644 Flagellar M-ring protein fliF (NCBI ptt file) 50, 492
BC1645 BC1645 Flagellar motor switch protein fliG (NCBI ptt file) 50, 492
BC1646 BC1646 hypothetical protein (NCBI ptt file) 462, 492
BC1647 BC1647 Flagellum-specific ATP synthase (NCBI ptt file) 50, 492
BC1649 BC1649 None 50, 492
BC1650 BC1650 Basal-body rod modification protein flgD (NCBI ptt file) 50, 492
BC1651 BC1651 Flagellar hook protein flgE (NCBI ptt file) 50, 492
BC1671 BC1671 Flagellar basal-body rod protein flgG (NCBI ptt file) 266, 462
BC1879 BC1879 Transglycosylase (NCBI ptt file) 50, 60
BC2257 BC2257 hypothetical protein (NCBI ptt file) 266, 462
BC2258 BC2258 Serine/threonine protein kinase (NCBI ptt file) 266, 462
BC2408 BC2408 ATP-dependent RNA helicase (NCBI ptt file) 213, 462
BC2443 BC2443 Transcriptional regulator, XRE family (NCBI ptt file) 50, 60
BC2667 BC2667 DEGV protein (NCBI ptt file) 213, 462
BC2710 BC2710 NADPH-dependent glutamate synthase beta chain and related oxidoreductases (NCBI ptt file) 460, 462
BC2721 BC2721 Serine/threonine protein kinases (NCBI ptt file) 213, 462
BC2723 BC2723 D-amino acid dehydrogenase small subunit (NCBI ptt file) 50, 283
BC2870 BC2870 Oligoendopeptidase F (NCBI ptt file) 50, 444
BC3058 BC3058 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 341, 462
BC3122 BC3122 Arylesterase (NCBI ptt file) 213, 462
BC3186 BC3186 hypothetical protein (NCBI ptt file) 213, 462
BC3678 BC3678 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 60, 462
BC3679 BC3679 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 60, 462
BC3811 BC3811 Bacterial Protein Translation Initiation Factor 2 (IF-2) (NCBI ptt file) 67, 462
BC3846 BC3846 Chromosome partition protein smc (NCBI ptt file) 92, 462
BC3874 BC3874 hypothetical protein (NCBI ptt file) 213, 462
BC5065 BC5065 Methyl-accepting chemotaxis protein (NCBI ptt file) 213, 462
BC5262 BC5262 Two-component response regulator (NCBI ptt file) 50, 283
BC5264 BC5264 EPSX protein (NCBI ptt file) 213, 462
BC5443 BC5443 Glycine betaine transporter (NCBI ptt file) 75, 462
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 BC0577
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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