Organism : Bacillus cereus ATCC14579 | Module List :
BC0333

IMP cyclohydrolase (NCBI ptt file)

CircVis
Functional Annotations (9)
Function System
AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) cog/ cog
IMP cyclohydrolase activity go/ molecular_function
phosphoribosylaminoimidazolecarboxamide formyltransferase activity go/ molecular_function
purine nucleotide biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
purH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0333
(Mouseover regulator name to see its description)

BC0333 is regulated by 12 influences and regulates 0 modules.
Regulators for BC0333 (12)
Regulator Module Operator
BC0042 179 tf
BC0840 179 tf
BC0848 179 tf
BC2358 179 tf
BC3690 179 tf
BC4091 179 tf
BC4170 179 tf
BC4703 179 tf
BC0776 416 tf
BC1033 416 tf
BC1363 416 tf
BC2122 416 tf

Warning: BC0333 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
4274 2.60e-05 AGGaGG
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4275 9.30e+03 CGgCTTgg
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4742 2.90e+03 CAGGGgG
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4743 1.60e+04 GGAcGAC
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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 BC0333

BC0333 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) cog/ cog
IMP cyclohydrolase activity go/ molecular_function
phosphoribosylaminoimidazolecarboxamide formyltransferase activity go/ molecular_function
purine nucleotide biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
purH tigr/ tigrfam
Module neighborhood information for BC0333

BC0333 has total of 25 gene neighbors in modules 179, 416
Gene neighbors (25)
Gene Common Name Description Module membership
BC0333 BC0333 IMP cyclohydrolase (NCBI ptt file) 179, 416
BC0986 BC0986 Response regulator aspartate phosphatase (NCBI ptt file) 20, 416
BC1050 BC1050 ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) 263, 416
BC1201 BC1201 None 76, 179
BC1250 BC1250 hypothetical protein (NCBI ptt file) 179, 468
BC1431 BC1431 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 20, 416
BC1575 BC1575 hypothetical protein (NCBI ptt file) 179, 484
BC1675 BC1675 Branched-chain amino acid transport protein azlD (NCBI ptt file) 218, 416
BC2098 BC2098 hypothetical protein (NCBI ptt file) 179, 186
BC2107 BC2107 Quinone oxidoreductase (NCBI ptt file) 86, 179
BC2117 BC2117 MoxR protein (NCBI ptt file) 179, 193
BC2208 BC2208 Iron(III) dicitrate-binding protein (NCBI ptt file) 389, 416
BC2328 BC2328 Pyruvate oxidase (NCBI ptt file) 96, 179
BC2606 BC2606 hypothetical Membrane Spanning Protein (NCBI ptt file) 225, 416
BC2857 BC2857 hypothetical protein (NCBI ptt file) 9, 416
BC3192 BC3192 Protein ydhR precursor (NCBI ptt file) 179, 321
BC3409 BC3409 Transcriptional regulator, MarR family (NCBI ptt file) 31, 179
BC3739 BC3739 Exodeoxyribonuclease III (NCBI ptt file) 225, 416
BC4164 BC4164 hypothetical protein (NCBI ptt file) 179, 506
BC4498 BC4498 ThiJ/PfpI family protein (NCBI ptt file) 108, 179
BC4569 BC4569 Multidrug resistance protein A (NCBI ptt file) 179, 285
BC5058 BC5058 Chloramphenicol resistance protein (NCBI ptt file) 179, 415
BC5126 BC5126 Transposase (NCBI ptt file) 416, 431
BC5424 BC5424 Methyl-accepting chemotaxis protein (NCBI ptt file) 416, 440
BC5446 BC5446 None 416, 440
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 BC0333
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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