Organism : Bacillus cereus ATCC14579 | Module List :
BC0323

Phosphoribosylaminoimidazole carboxylase catalytic subunit (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase cog/ cog
phosphoribosylaminoimidazole carboxylase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
phosphoribosylaminoimidazole carboxylase complex go/ cellular_component
Purine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
purE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0323
(Mouseover regulator name to see its description)

BC0323 is regulated by 28 influences and regulates 0 modules.
Regulators for BC0323 (28)
Regulator Module Operator
BC0116 283 tf
BC0123 283 tf
BC0410 283 tf
BC0473 283 tf
BC0613 283 tf
BC2794 283 tf
BC3095 283 tf
BC3792 283 tf
BC3826 283 tf
BC4057 283 tf
BC4091 283 tf
BC4603 283 tf
BC5205 283 tf
BC5250 283 tf
BC0122 92 tf
BC0595 92 tf
BC0598 92 tf
BC0993 92 tf
BC1337 92 tf
BC1363 92 tf
BC2218 92 tf
BC2979 92 tf
BC3128 92 tf
BC3814 92 tf
BC3826 92 tf
BC3922 92 tf
BC4652 92 tf
BC5265 92 tf

Warning: BC0323 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
4100 1.10e-01 GGGGgA
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4101 4.80e+00 CCTtgTgaataGAatgctaac
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4482 2.30e-03 agaGagGG
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4483 8.50e+03 aAaAgaGa
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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 BC0323

BC0323 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase cog/ cog
phosphoribosylaminoimidazole carboxylase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
phosphoribosylaminoimidazole carboxylase complex go/ cellular_component
Purine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
purE tigr/ tigrfam
Module neighborhood information for BC0323

BC0323 has total of 40 gene neighbors in modules 92, 283
Gene neighbors (40)
Gene Common Name Description Module membership
BC0121 BC0121 16S rRNA m(2)G 1207 methyltransferase (NCBI ptt file) 92, 366
BC0258 BC0258 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D- alanyl ligase (NCBI ptt file) 283, 311
BC0297 BC0297 Guanine-hypoxanthine permease (NCBI ptt file) 234, 283
BC0323 BC0323 Phosphoribosylaminoimidazole carboxylase catalytic subunit (NCBI ptt file) 92, 283
BC0324 BC0324 Phosphoribosylaminoimidazole carboxylase ATPase subunit (NCBI ptt file) 92, 283
BC0325 BC0325 Adenylosuccinate lyase (NCBI ptt file) 92, 283
BC0631 BC0631 PTS system, trehalose-specific IIBC component (NCBI ptt file) 283, 387
BC0632 BC0632 Trehalose-6-phosphate hydrolase (NCBI ptt file) 283, 387
BC1068 BC1068 Uroporphyrinogen decarboxylase (NCBI ptt file) 283, 311
BC1247 BC1247 hypothetical protein (NCBI ptt file) 92, 432
BC1369 BC1369 Protein dltD precursor (NCBI ptt file) 201, 283
BC1370 BC1370 D-alanyl carrier protein (NCBI ptt file) 201, 283
BC1565 BC1565 ATP-dependent helicase, DinG family (NCBI ptt file) 92, 458
BC1569 BC1569 Xanthine phosphoribosyltransferase (NCBI ptt file) 234, 283
BC1570 BC1570 Xanthine permease (NCBI ptt file) 234, 283
BC1615 BC1615 Na+ driven multidrug efflux pump (NCBI ptt file) 92, 103
BC1793 BC1793 Chlorohydrolase/deaminase family protein (NCBI ptt file) 92, 133
BC2021 BC2021 High-affinity zinc uptake system protein znuA precursor (NCBI ptt file) 92, 133
BC2722 BC2722 dATP pyrophosphohydrolase (NCBI ptt file) 38, 283
BC2723 BC2723 D-amino acid dehydrogenase small subunit (NCBI ptt file) 50, 283
BC3177 BC3177 DNA helicase (NCBI ptt file) 92, 143
BC3707 BC3707 Aluminum resistance protein (NCBI ptt file) 236, 283
BC3790 BC3790 Nucleoside transport ATP-binding protein (NCBI ptt file) 234, 283
BC3791 BC3791 Nucleoside-binding protein (NCBI ptt file) 234, 283
BC3792 BC3792 Transcriptional regulator, GntR family (NCBI ptt file) 234, 283
BC3845 BC3845 Cell division protein ftsY (NCBI ptt file) 92, 476
BC3846 BC3846 Chromosome partition protein smc (NCBI ptt file) 92, 462
BC3912 BC3912 UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI ptt file) 283, 382
BC3916 BC3916 Division specific D,D-transpeptidase / Cell division protein ftsI (NCBI ptt file) 283, 479
BC3922 BC3922 Prespore specific transcriptional activator rsfA (NCBI ptt file) 92, 142
BC4083 BC4083 Guanine-hypoxanthine permease (NCBI ptt file) 283, 290
BC4507 BC4507 Aquaporin (NCBI ptt file) 92, 133
BC5012 BC5012 Chloramphenicol resistance protein (NCBI ptt file) 92, 133
BC5158 BC5158 Integral membrane protein (NCBI ptt file) 92, 214
BC5218 BC5218 Proton/sodium-glutamate symport protein (NCBI ptt file) 92, 458
BC5235 BC5235 Nucleoside permease nupC (NCBI ptt file) 92, 133
BC5259 BC5259 ABC transporter substrate-binding protein (NCBI ptt file) 213, 283
BC5260 BC5260 hypothetical Exported Protein (NCBI ptt file) 283, 290
BC5261 BC5261 Two component system histidine kinase (NCBI ptt file) 213, 283
BC5262 BC5262 Two-component response regulator (NCBI ptt file) 50, 283
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 BC0323
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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