Organism : Bacillus cereus ATCC14579 | Module List :
BC3687

2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases cog/ cog
2',3'-cyclic-nucleotide 2'-phosphodiesterase activity go/ molecular_function
nucleotide catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3687
(Mouseover regulator name to see its description)

BC3687 is regulated by 20 influences and regulates 0 modules.
Regulators for BC3687 (20)
Regulator Module Operator
BC0518 453 tf
BC0882 453 tf
BC1673 453 tf
BC2379 453 tf
BC2526 453 tf
BC2742 453 tf
BC2904 453 tf
BC3389 453 tf
BC3493 453 tf
BC4101 453 tf
BC4650 453 tf
BC0993 209 tf
BC1698 209 tf
BC2770 209 tf
BC2971 209 tf
BC4072 209 tf
BC4289 209 tf
BC4433 209 tf
BC5332 209 tf
BC5402 209 tf

Warning: BC3687 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
4334 3.50e+01 TGaAgAgG
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4335 2.00e+03 GGGGGC
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4816 9.00e+04 GAGGTGAGaG
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4817 3.00e+03 TaGGGGta
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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 BC3687

BC3687 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases cog/ cog
2',3'-cyclic-nucleotide 2'-phosphodiesterase activity go/ molecular_function
nucleotide catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Module neighborhood information for BC3687

BC3687 has total of 47 gene neighbors in modules 209, 453
Gene neighbors (47)
Gene Common Name Description Module membership
BC0372 BC0372 hypothetical protein (NCBI ptt file) 249, 453
BC0447 BC0447 Tellurite resistance protein (NCBI ptt file) 13, 209
BC0687 BC0687 IG hypothetical 22578 (NCBI ptt file) 453, 509
BC0882 BC0882 Two-component response regulator comA (NCBI ptt file) 85, 453
BC0932 BC0932 hypothetical protein (NCBI ptt file) 256, 453
BC1065 BC1065 hypothetical Membrane Spanning Protein (NCBI ptt file) 30, 453
BC1210 BC1210 hypothetical protein (NCBI ptt file) 209, 276
BC1265 BC1265 hypothetical Cytosolic Protein (NCBI ptt file) 453, 509
BC1736 BC1736 Export ABC transporter permease protein (NCBI ptt file) 209, 281
BC1788 BC1788 Lysophospholipase L2 (NCBI ptt file) 209, 253
BC1943 BC1943 Glycosyltransferase (NCBI ptt file) 239, 453
BC1999 BC1999 IolS protein (NCBI ptt file) 108, 453
BC2090 BC2090 hypothetical protein (NCBI ptt file) 254, 453
BC2189 BC2189 Aminoglycoside phosphotransferase (NCBI ptt file) 209, 407
BC2326 BC2326 Oligopeptide transport system permease protein oppB (NCBI ptt file) 163, 209
BC2330 BC2330 Zn-dependent hydrolase (NCBI ptt file) 453, 460
BC2348 BC2348 Acetyltransferase (NCBI ptt file) 163, 453
BC2363 BC2363 Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 123, 453
BC2407 BC2407 hypothetical protein (NCBI ptt file) 286, 453
BC2430 BC2430 Methyltransferase (NCBI ptt file) 217, 453
BC2583 BC2583 Terminase large subunit (NCBI ptt file) 209, 223
BC2629 BC2629 Methionyl-tRNA formyltransferase (NCBI ptt file) 209, 253
BC2742 BC2742 Transcriptional regulator, GntR family (NCBI ptt file) 9, 453
BC2810 BC2810 hypothetical protein (NCBI ptt file) 321, 453
BC2915 BC2915 hypothetical protein (NCBI ptt file) 55, 453
BC2923 BC2923 Acetyltransferase (NCBI ptt file) 193, 453
BC3014 BC3014 hypothetical protein (NCBI ptt file) 72, 453
BC3029 BC3029 hypothetical protein (NCBI ptt file) 209, 453
BC3150 BC3150 Transcriptional regulator, AraC family (NCBI ptt file) 359, 453
BC3170 BC3170 Transposase (NCBI ptt file) 453, 461
BC3188 BC3188 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 163, 209
BC3216 BC3216 1-aminocyclopropane-1-carboxylate deaminase (NCBI ptt file) 72, 453
BC3265 BC3265 hypothetical Cytosolic Protein (NCBI ptt file) 24, 209
BC3322 BC3322 hypothetical protein (NCBI ptt file) 197, 453
BC3349 BC3349 Transporter, MFS superfamily (NCBI ptt file) 209, 415
BC3366 BC3366 oxetanocin A resistance protein (NCBI ptt file) 254, 453
BC3446 BC3446 hypothetical protein (NCBI ptt file) 428, 453
BC3457 BC3457 hypothetical protein (NCBI ptt file) 62, 453
BC3487 BC3487 hypothetical protein (NCBI ptt file) 175, 209
BC3625 BC3625 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 26, 209
BC3687 BC3687 2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI ptt file) 209, 453
BC3919 BC3919 hypothetical Membrane Spanning Protein (NCBI ptt file) 288, 453
BC4818 BC4818 hypothetical protein (NCBI ptt file) 246, 453
BC4839 BC4839 ABC transporter ATP-binding protein (NCBI ptt file) 63, 453
BC5031 BC5031 Methionyl-tRNA synthetase (NCBI ptt file) 408, 453
BC5036 BC5036 Bacillolysin (NCBI ptt file) 209, 504
BC5049 BC5049 hypothetical Membrane Spanning Protein (NCBI ptt file) 146, 209
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 BC3687
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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