Organism : Bacillus cereus ATCC14579 | Module List :
BC4111

GTP cyclohydrolase II (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
3,4-dihydroxy-2-butanone 4-phosphate synthase cog/ cog
GTP cyclohydrolase II activity go/ molecular_function
3,4-dihydroxy-2-butanone-4-phosphate synthase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ribA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4111
(Mouseover regulator name to see its description)

BC4111 is regulated by 33 influences and regulates 0 modules.
Regulators for BC4111 (33)
Regulator Module Operator
BC0851 512 tf
BC0975 512 tf
BC1134 512 tf
BC1814 512 tf
BC1915 512 tf
BC2217 512 tf
BC2353 512 tf
BC2631 512 tf
BC2760 512 tf
BC3033 512 tf
BC3155 512 tf
BC3175 512 tf
BC3405 512 tf
BC4081 512 tf
BC4206 512 tf
BC4499 512 tf
BC4589 512 tf
BC5265 512 tf
BC5409 512 tf
BC0595 77 tf
BC0954 77 tf
BC1356 77 tf
BC1363 77 tf
BC2738 77 tf
BC2794 77 tf
BC2914 77 tf
BC3253 77 tf
BC3405 77 tf
BC3891 77 tf
BC4072 77 tf
BC4081 77 tf
BC4104 77 tf
BC5171 77 tf

Warning: BC4111 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
4074 2.90e+02 GGaGGGActa
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4075 7.60e+03 CTCCcAtA
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4934 1.20e-03 GGGGGa
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4935 7.20e+03 CtGcaGGGC
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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 BC4111

BC4111 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
3,4-dihydroxy-2-butanone 4-phosphate synthase cog/ cog
GTP cyclohydrolase II activity go/ molecular_function
3,4-dihydroxy-2-butanone-4-phosphate synthase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
ribA tigr/ tigrfam
Module neighborhood information for BC4111

BC4111 has total of 42 gene neighbors in modules 77, 512
Gene neighbors (42)
Gene Common Name Description Module membership
BC0403 BC0403 Glutamine transport ATP-binding protein glnQ (NCBI ptt file) 487, 512
BC0666 BC0666 Immune inhibitor A precursor (NCBI ptt file) 171, 512
BC0753 BC0753 Potassium-transporting ATPase A chain (NCBI ptt file) 282, 512
BC0754 BC0754 Potassium-transporting ATPase B chain (NCBI ptt file) 282, 512
BC0755 BC0755 Potassium-transporting ATPase C chain (NCBI ptt file) 282, 512
BC0756 BC0756 Sensor protein kdpD (NCBI ptt file) 282, 512
BC0849 BC0849 Amino acid acetyltransferase (NCBI ptt file) 282, 512
BC1994 BC1994 NH(3)-dependent NAD(+) synthetase (NCBI ptt file) 47, 77
BC2038 BC2038 Acyl-CoA hydrolase (NCBI ptt file) 59, 77
BC2311 BC2311 4'-phosphopantetheinyl transferase (NCBI ptt file) 47, 77
BC2312 BC2312 hypothetical protein (NCBI ptt file) 47, 77
BC2661 BC2661 Bacitracin transport permease protein BCRC (NCBI ptt file) 47, 77
BC2958 BC2958 hypothetical protein (NCBI ptt file) 77, 525
BC2969 BC2969 hypothetical protein (NCBI ptt file) 48, 77
BC3031 BC3031 Isoflavone reductase (NCBI ptt file) 484, 512
BC3346 BC3346 Collagen-like triple helix repeat protein (NCBI ptt file) 359, 512
BC3483 BC3483 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 77, 233
BC3527 BC3527 hypothetical protein (NCBI ptt file) 77, 171
BC3743 BC3743 Peptidase T (NCBI ptt file) 77, 233
BC4109 BC4109 Diaminohydroxyphosphoribosylaminopyrimidine deaminase (NCBI ptt file) 77, 512
BC4110 BC4110 Riboflavin synthase alpha chain (NCBI ptt file) 77, 512
BC4111 BC4111 GTP cyclohydrolase II (NCBI ptt file) 77, 512
BC4112 BC4112 6,7-dimethyl-8-ribityllumazine synthase (NCBI ptt file) 77, 512
BC4126 BC4126 Ornithine carbamoyltransferase (NCBI ptt file) 282, 512
BC4127 argD acetylornithine aminotransferase (RefSeq) 282, 512
BC4128 BC4128 Acetylglutamate kinase (NCBI ptt file) 282, 512
BC4129 BC4129 Glutamate N-acetyltransferase (NCBI ptt file) 282, 512
BC4130 BC4130 None 282, 512
BC4148 BC4148 Arginine transport ATP-binding protein artP (NCBI ptt file) 282, 512
BC4149 BC4149 Arginine transport system permease protein artQ (NCBI ptt file) 282, 512
BC4150 BC4150 Arginine-binding protein (NCBI ptt file) 282, 512
BC4543 BC4543 hypothetical Exported Protein (NCBI ptt file) 77, 419
BC4544 BC4544 Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) 77, 419
BC4545 BC4545 Ferrichrome transport system permease protein fhuB (NCBI ptt file) 77, 419
BC4546 BC4546 Ferrichrome-binding protein (NCBI ptt file) 77, 419
BC4547 BC4547 Cell surface protein (NCBI ptt file) 77, 419
BC4548 BC4548 Cell surface protein (NCBI ptt file) 77, 271
BC4549 BC4549 Cell surface protein (NCBI ptt file) 77, 271
BC4628 BC4628 hypothetical protein (NCBI ptt file) 282, 512
BC4629 BC4629 Argininosuccinate lyase (NCBI ptt file) 282, 512
BC4630 BC4630 Argininosuccinate synthase (NCBI ptt file) 282, 512
BC5181 BC5181 hypothetical protein (NCBI ptt file) 76, 77
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 BC4111
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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