Organism : Bacillus cereus ATCC14579 | Module List :
BC4250

5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file)

CircVis
Functional Annotations (14)
Function System
Methionine synthase I, cobalamin-binding domain cog/ cog
dihydropteroate synthase activity go/ molecular_function
intracellular go/ cellular_component
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
folic acid-containing compound biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
cobalt ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
metH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4250
(Mouseover regulator name to see its description)

BC4250 is regulated by 35 influences and regulates 0 modules.
Regulators for BC4250 (35)
Regulator Module Operator
BC0607 318 tf
BC0848 318 tf
BC0856 318 tf
BC1427 318 tf
BC1732 318 tf
BC2351 318 tf
BC2401 318 tf
BC2979 318 tf
BC3128 318 tf
BC3155 318 tf
BC3190 318 tf
BC3405 318 tf
BC3493 318 tf
BC4076 318 tf
BC4474 318 tf
BC4826 318 tf
BC5143 318 tf
BC0607 338 tf
BC0806 338 tf
BC0848 338 tf
BC0856 338 tf
BC1037 338 tf
BC1427 338 tf
BC1936 338 tf
BC2351 338 tf
BC2401 338 tf
BC2815 338 tf
BC2964 338 tf
BC3155 338 tf
BC3320 338 tf
BC3405 338 tf
BC3756 338 tf
BC4826 338 tf
BC5176 338 tf
BC5361 338 tf

Warning: BC4250 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
4550 1.10e-15 gacACGGTGCTAATTCcaGCAa
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4551 1.40e-04 tTGAaAGATAAGagggagg
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4588 5.70e-04 ggcacGgtgCTAattCcagCa
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4589 9.20e-03 AAaaGggGggG
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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 BC4250

BC4250 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Methionine synthase I, cobalamin-binding domain cog/ cog
dihydropteroate synthase activity go/ molecular_function
intracellular go/ cellular_component
methionine synthase activity go/ molecular_function
homocysteine S-methyltransferase activity go/ molecular_function
methionine biosynthetic process go/ biological_process
folic acid-containing compound biosynthetic process go/ biological_process
cobalamin binding go/ molecular_function
cobalt ion binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
metH tigr/ tigrfam
Module neighborhood information for BC4250

BC4250 has total of 30 gene neighbors in modules 318, 338
Gene neighbors (30)
Gene Common Name Description Module membership
BC0207 BC0207 Oligopeptide transport system permease protein oppB (NCBI ptt file) 318, 408
BC0208 BC0208 Oligopeptide transport system permease protein oppC (NCBI ptt file) 53, 318
BC0209 BC0209 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 53, 318
BC0210 BC0210 Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) 53, 318
BC0211 BC0211 Oligopeptide-binding protein oppA (NCBI ptt file) 318, 408
BC0767 BC0767 Methylthioribose transport ATP-binding protein (NCBI ptt file) 318, 338
BC0768 BC0768 Methylthioribose-binding protein (NCBI ptt file) 318, 338
BC0794 BC0794 Hydroxyacylglutathione hydrolase (NCBI ptt file) 338, 523
BC0795 BC0795 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 338, 523
BC0796 BC0796 Rhodanese-related sulfurtransferases (NCBI ptt file) 338, 523
BC0797 BC0797 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 338, 523
BC0798 BC0798 NADH dehydrogenase (NCBI ptt file) 338, 523
BC0799 BC0799 hypothetical Membrane Spanning Protein (NCBI ptt file) 244, 338
BC1365 BC1365 Isochorismatase (NCBI ptt file) 338, 523
BC1419 BC1419 Diaminopimelate decarboxylase (NCBI ptt file) 282, 338
BC1420 BC1420 hypothetical protein (NCBI ptt file) 338, 509
BC1426 BC1426 Uroporphyrin-III C-methyltransferase (NCBI ptt file) 338, 514
BC3159 BC3159 NAD-dependent epimerase/dehydratase / Alpha/beta hydrolase (NCBI ptt file) 38, 338
BC3172 BC3172 hypothetical protein (NCBI ptt file) 186, 338
BC3176 BC3176 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 318, 408
BC4031 BC4031 hypothetical protein (NCBI ptt file) 23, 338
BC4032 BC4032 Methylthioribose salvage protein (NCBI ptt file) 318, 338
BC4033 BC4033 5-methylthioribose kinase (NCBI ptt file) 318, 408
BC4038 BC4038 Methylthioribose salvage protein (putative aldolase) (NCBI ptt file) 53, 318
BC4040 BC4040 hypothetical Membrane Spanning Protein (NCBI ptt file) 338, 358
BC4250 BC4250 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file) 318, 338
BC4251 BC4251 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file) 205, 338
BC4253 BC4253 Cystathionine gamma-synthase (NCBI ptt file) 215, 318
BC5404 BC5404 Homoserine dehydrogenase (NCBI ptt file) 338, 408
BC5405 BC5405 Homoserine O-succinyltransferase (NCBI ptt file) 338, 521
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 BC4250
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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