Organism : Bacillus cereus ATCC14579 | Module List :
BC3962

Arginine decarboxylase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Arginine/lysine/ornithine decarboxylases cog/ cog
lysine decarboxylase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3962
(Mouseover regulator name to see its description)

BC3962 is regulated by 23 influences and regulates 0 modules.
Regulators for BC3962 (23)
Regulator Module Operator
BC0607 159 tf
BC0742 159 tf
BC1439 159 tf
BC1889 159 tf
BC3982 159 tf
BC4010 159 tf
BC4057 159 tf
BC4316 159 tf
BC5361 159 tf
BC5481 159 tf
BC0801 260 tf
BC0840 260 tf
BC1329 260 tf
BC1489 260 tf
BC1987 260 tf
BC2401 260 tf
BC2964 260 tf
BC3160 260 tf
BC3982 260 tf
BC5200 260 tf
BC5339 260 tf
BC5340 260 tf
BC5463 260 tf

Warning: BC3962 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
4234 7.60e+00 TAgatAAaaaaGtGa
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4235 1.90e+03 AatagAAggga
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4436 4.20e+03 CATccCCatCc
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4437 3.30e+01 AaGaAGaaaaggtgc
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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 BC3962

BC3962 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Arginine/lysine/ornithine decarboxylases cog/ cog
lysine decarboxylase activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BC3962

BC3962 has total of 36 gene neighbors in modules 159, 260
Gene neighbors (36)
Gene Common Name Description Module membership
BC0050 BC0050 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (NCBI ptt file) 260, 406
BC0256 BC0256 Multidrug resistance protein B (NCBI ptt file) 159, 433
BC0607 BC0607 Transcriptional regulator, LytR family (NCBI ptt file) 159, 432
BC0628 BC0628 Sensory box/GGDEF family protein (NCBI ptt file) 6, 260
BC0897 BC0897 hypothetical protein (NCBI ptt file) 159, 442
BC1044 BC1044 hypothetical protein (NCBI ptt file) 6, 260
BC1276 BC1276 hypothetical protein (NCBI ptt file) 6, 260
BC1512 BC1512 Heptaprenyl diphosphate synthase component I (NCBI ptt file) 260, 273
BC1513 BC1513 2-heptaprenyl-1,4-naphthoquinone methyltransferase (NCBI ptt file) 6, 260
BC1514 BC1514 Farnesyltransferase (NCBI ptt file) 260, 482
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC1948 BC1948 hypothetical Multidrug-Efflux Transporter (NCBI ptt file) 159, 433
BC1949 BC1949 hypothetical protein (NCBI ptt file) 159, 433
BC1951 BC1951 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 159, 442
BC1970 BC1970 hypothetical protein (NCBI ptt file) 76, 159
BC1971 BC1971 hypothetical protein (NCBI ptt file) 159, 177
BC1972 BC1972 Alkaline phosphatase synthesis two-component response regulator phoP (NCBI ptt file) 159, 177
BC1973 BC1973 Two component system histidine kinase (NCBI ptt file) 159, 177
BC2036 BC2036 hypothetical Membrane Spanning Protein (NCBI ptt file) 159, 329
BC2096 BC2096 hypothetical protein (NCBI ptt file) 148, 260
BC2172 BC2172 IG hypothetical 18880 (NCBI ptt file) 55, 159
BC2173 BC2173 hypothetical Membrane Spanning Protein (NCBI ptt file) 55, 159
BC2234 BC2234 Arginine/ornithine antiporter (NCBI ptt file) 159, 399
BC2846 BC2846 Protein dltD precursor (NCBI ptt file) 159, 223
BC3160 BC3160 Transcriptional regulator, TetR family (NCBI ptt file) 243, 260
BC3641 BC3641 Sensor protein atoS (NCBI ptt file) 6, 260
BC3854 BC3854 Predicted kinase related to hydroxyacetone kinase (NCBI ptt file) 260, 371
BC3930 BC3930 Methyltransferase (NCBI ptt file) 243, 260
BC3948 BC3948 Cell division protein ftsW (NCBI ptt file) 243, 260
BC3962 BC3962 Arginine decarboxylase (NCBI ptt file) 159, 260
BC4261 BC4261 hypothetical Cytosolic Protein (NCBI ptt file) 260, 406
BC4335 BC4335 Phosphatidylserine decarboxylase (NCBI ptt file) 159, 433
BC4379 BC4379 hypothetical protein (NCBI ptt file) 159, 433
BC5097 BC5097 Leucine-responsive regulatory protein (NCBI ptt file) 260, 302
BC5196 BC5196 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 260, 390
BC5198 BC5198 DegV family protein (NCBI ptt file) 170, 260
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 BC3962
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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