Organism : Bacillus cereus ATCC14579 | Module List :
BC1449

cAMP-dependent protein kinase regulatory chain (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1449
(Mouseover regulator name to see its description)

BC1449 is regulated by 23 influences and regulates 9 modules.
Regulators for BC1449 (23)
Regulator Module Operator
BC0047 217 tf
BC0230 217 tf
BC0648 217 tf
BC0856 217 tf
BC1449 217 tf
BC1703 217 tf
BC1884 217 tf
BC3593 217 tf
BC3720 217 tf
BC3903 217 tf
BC4256 217 tf
BC4336 217 tf
BC5010 217 tf
BC5222 217 tf
BC5250 217 tf
BC0742 504 tf
BC2410 504 tf
BC3253 504 tf
BC3903 504 tf
BC4499 504 tf
BC5173 504 tf
BC5200 504 tf
BC5205 504 tf

Warning: BC1449 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
4350 6.20e-07 aagaaagGaGa
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4351 9.40e+02 CCcTCC
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4918 8.90e+02 agaggGGG
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4919 7.10e+00 CATaTAcgcTAAaatAGaAgAA
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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 BC1449

BC1449 is enriched for 4 functions in 3 categories.
Module neighborhood information for BC1449

BC1449 has total of 55 gene neighbors in modules 217, 504
Gene neighbors (55)
Gene Common Name Description Module membership
BC0034 BC0034 CsfB protein (NCBI ptt file) 217, 351
BC0047 BC0047 Sporulation-specific protease YabG (NCBI ptt file) 217, 393
BC0288 BC0288 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 217, 351
BC0384 BC0384 hypothetical protein (NCBI ptt file) 48, 504
BC0480 BC0480 hypothetical protein (NCBI ptt file) 217, 241
BC0818 BC0818 Oligopeptide transport system permease protein oppB (NCBI ptt file) 217, 351
BC0819 BC0819 Oligopeptide transport system permease protein oppC (NCBI ptt file) 162, 217
BC0870 BC0870 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 104, 217
BC0871 BC0871 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 104, 217
BC1088 BC1088 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 317, 504
BC1141 BC1141 Spore germination protein PE (NCBI ptt file) 217, 351
BC1152 BC1152 Asparagine synthetase (NCBI ptt file) 136, 217
BC1153 BC1153 Asparagine synthetase (NCBI ptt file) 397, 504
BC1243 BC1243 hypothetical protein (NCBI ptt file) 217, 377
BC1331 BC1331 Internalin (NCBI ptt file) 217, 419
BC1449 BC1449 cAMP-dependent protein kinase regulatory chain (NCBI ptt file) 217, 504
BC1450 BC1450 hypothetical protein (NCBI ptt file) 241, 504
BC1568 BC1568 Methionine aminopeptidase (NCBI ptt file) 217, 407
BC1830 BC1830 Copper resistance protein A (NCBI ptt file) 123, 217
BC1978 BC1978 Siderophore biosynthesis protein (NCBI ptt file) 46, 504
BC1982 BC1982 hypothetical protein (NCBI ptt file) 504, 520
BC1983 BC1983 hypothetical Cytosolic Protein (NCBI ptt file) 46, 504
BC2043 BC2043 IG hypothetical 17883 (NCBI ptt file) 303, 504
BC2239 BC2239 hypothetical protein (NCBI ptt file) 26, 504
BC2378 BC2378 Transporter, LysE family (NCBI ptt file) 217, 509
BC2404 BC2404 hypothetical Cytosolic Protein (NCBI ptt file) 217, 241
BC2417 BC2417 hypothetical protein (NCBI ptt file) 123, 217
BC2430 BC2430 Methyltransferase (NCBI ptt file) 217, 453
BC2465 BC2465 hypothetical protein (NCBI ptt file) 85, 217
BC2544 BC2544 ABC transporter permease protein (NCBI ptt file) 217, 351
BC2545 BC2545 hypothetical protein (NCBI ptt file) 136, 217
BC2559 BC2559 Phage protein (NCBI ptt file) 184, 504
BC2711 BC2711 Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file) 2, 217
BC2741 BC2741 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 76, 217
BC2744 BC2744 hypothetical protein (NCBI ptt file) 158, 217
BC2790 BC2790 Glycine betaine transport system permease protein (NCBI ptt file) 397, 504
BC3191 BC3191 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 125, 504
BC3280 BC3280 hypothetical protein (NCBI ptt file) 136, 217
BC3474 BC3474 hypothetical protein (NCBI ptt file) 217, 351
BC3475 BC3475 hypothetical protein (NCBI ptt file) 3, 217
BC3488 BC3488 hypothetical Membrane Spanning Protein (NCBI ptt file) 502, 504
BC3489 BC3489 Agmatine deiminase (NCBI ptt file) 502, 504
BC3593 BC3593 Transcriptional regulator, DeoR family (NCBI ptt file) 217, 351
BC3667 BC3667 ABC transporter permease protein (NCBI ptt file) 2, 217
BC3967 BC3967 hypothetical protein (NCBI ptt file) 154, 217
BC4304 BC4304 hypothetical Cytosolic Protein (NCBI ptt file) 217, 272
BC4520 uvrC excinuclease ABC subunit C (RefSeq) 217, 351
BC4529 BC4529 None 184, 504
BC4607 BC4607 hypothetical protein (NCBI ptt file) 217, 339
BC4641 BC4641 hypothetical protein (NCBI ptt file) 154, 217
BC4784 BC4784 hypothetical protein (NCBI ptt file) 199, 504
BC4847 BC4847 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 217, 361
BC4858 BC4858 DnaK suppressor protein (NCBI ptt file) 217, 241
BC5036 BC5036 Bacillolysin (NCBI ptt file) 209, 504
BC5173 BC5173 Transcriptional regulator, PBSX family (NCBI ptt file) 184, 504
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 BC1449
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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