Organism : Bacillus cereus ATCC14579 | Module List :
BC3121

5'-nucleotidase (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases cog/ cog
5'-nucleotidase activity go/ molecular_function
nucleotide catabolic process go/ biological_process
IMP-GMP specific 5'-nucleotidase activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3121
(Mouseover regulator name to see its description)

BC3121 is regulated by 22 influences and regulates 0 modules.
Regulators for BC3121 (22)
Regulator Module Operator
BC0099 428 tf
BC0975 428 tf
BC1363 428 tf
BC2122 428 tf
BC2218 428 tf
BC2386 428 tf
BC2526 428 tf
BC2742 428 tf
BC3175 428 tf
BC5175 428 tf
BC0099 214 tf
BC0613 214 tf
BC0954 214 tf
BC1080 214 tf
BC1302 214 tf
BC1363 214 tf
BC2218 214 tf
BC3095 214 tf
BC3706 214 tf
BC3826 214 tf
BC4081 214 tf
BC5000 214 tf

Warning: BC3121 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
4344 7.20e-13 aaaAggGGAga
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4345 6.10e+03 CAGTGGGGG
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4766 5.50e-07 aataaaaGgAG
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4767 4.70e+03 GgacGgGaga
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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 BC3121

BC3121 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases cog/ cog
5'-nucleotidase activity go/ molecular_function
nucleotide catabolic process go/ biological_process
IMP-GMP specific 5'-nucleotidase activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for BC3121

BC3121 has total of 50 gene neighbors in modules 214, 428
Gene neighbors (50)
Gene Common Name Description Module membership
BC0127 BC0127 None 214, 396
BC0171 BC0171 Chitooligosaccharide deacetylase (NCBI ptt file) 158, 428
BC0629 BC0629 Arginine/ornithine antiporter (NCBI ptt file) 134, 428
BC0888 BC0888 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 214, 382
BC0959 BC0959 hypothetical Membrane Spanning Protein (NCBI ptt file) 37, 214
BC1124 BC1124 Methyl-accepting chemotaxis protein (NCBI ptt file) 428, 489
BC1156 BC1156 Ammonium transporter (NCBI ptt file) 214, 481
BC1254 BC1254 hypothetical protein (NCBI ptt file) 9, 428
BC1259 BC1259 hypothetical protein (NCBI ptt file) 62, 214
BC1363 BC1363 Leucine-responsive regulatory protein (NCBI ptt file) 204, 428
BC1571 BC1571 hypothetical Membrane Spanning Protein (NCBI ptt file) 204, 214
BC1577 BC1577 hypothetical protein (NCBI ptt file) 428, 481
BC1628 BC1628 Chemotaxis protein cheA (NCBI ptt file) 214, 517
BC1639 BC1639 Flagellar protein fliS (NCBI ptt file) 214, 396
BC1654 BC1654 Chemotaxis protein cheV (NCBI ptt file) 157, 428
BC1676 BC1676 hypothetical protein (NCBI ptt file) 312, 428
BC1677 BC1677 Dienelactone hydrolase family (NCBI ptt file) 141, 428
BC1752 BC1752 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 214, 428
BC1767 BC1767 Sodium-dependent serine transporter (NCBI ptt file) 412, 428
BC2059 BC2059 Phosphoglycerate mutase (NCBI ptt file) 62, 428
BC2060 BC2060 hydrolase (HAD superfamily) (NCBI ptt file) 62, 428
BC2061 BC2061 Multidrug resistance protein B (NCBI ptt file) 256, 428
BC2218 BC2218 Transcriptional regulator, RpiR family (NCBI ptt file) 214, 517
BC2261 BC2261 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 100, 214
BC2333 BC2333 hypothetical protein (NCBI ptt file) 214, 266
BC2526 BC2526 Transcriptional regulator, GntR family (NCBI ptt file) 30, 428
BC2699 BC2699 None 139, 428
BC3121 BC3121 5'-nucleotidase (NCBI ptt file) 214, 428
BC3146 BC3146 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 9, 428
BC3175 BC3175 Leucine-responsive regulatory protein (NCBI ptt file) 364, 428
BC3210 BC3210 hypothetical Cytosolic Protein (NCBI ptt file) 312, 428
BC3250 BC3250 hypothetical protein (NCBI ptt file) 214, 341
BC3398 BC3398 Serine transporter (NCBI ptt file) 214, 481
BC3446 BC3446 hypothetical protein (NCBI ptt file) 428, 453
BC3506 BC3506 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 246, 428
BC3507 BC3507 hypothetical protein (NCBI ptt file) 428, 481
BC3639 BC3639 hypothetical Membrane Spanning Protein (NCBI ptt file) 214, 428
BC4216 BC4216 hypothetical protein (NCBI ptt file) 341, 428
BC4352 BC4352 Phenylalanine-4-hydroxylase (NCBI ptt file) 158, 428
BC4687 BC4687 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 214, 341
BC4708 BC4708 Transcriptional regulator, ArsR family (NCBI ptt file) 198, 214
BC4709 BC4709 hypothetical protein (NCBI ptt file) 198, 214
BC4812 BC4812 Cell surface protein (NCBI ptt file) 158, 428
BC4944 BC4944 hypothetical protein (NCBI ptt file) 214, 481
BC5000 BC5000 Transcriptional regulator, TetR family (NCBI ptt file) 214, 341
BC5001 BC5001 Metal-dependent hydrolase (NCBI ptt file) 214, 341
BC5034 BC5034 Methyl-accepting chemotaxis protein (NCBI ptt file) 214, 266
BC5158 BC5158 Integral membrane protein (NCBI ptt file) 92, 214
BC5263 BC5263 UDP-glucose 4-epimerase (NCBI ptt file) 204, 214
BC5428 BC5428 hypothetical protein (NCBI ptt file) 341, 428
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 BC3121
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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