Organism : Bacillus cereus ATCC14579 | Module List :
BC3031

Isoflavone reductase (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Nucleoside-diphosphate-sugar epimerases cog/ cog
catalytic activity go/ molecular_function
cellular metabolic process go/ biological_process
2'-hydroxyisoflavone reductase activity go/ molecular_function
coenzyme binding go/ molecular_function
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3031
(Mouseover regulator name to see its description)

BC3031 is regulated by 34 influences and regulates 0 modules.
Regulators for BC3031 (34)
Regulator Module Operator
BC0657 484 tf
BC1335 484 tf
BC1818 484 tf
BC1884 484 tf
BC2469 484 tf
BC2517 484 tf
BC2558 484 tf
BC2837 484 tf
BC3224 484 tf
BC3690 484 tf
BC4001 484 tf
BC4170 484 tf
BC4670 484 tf
BC5024 484 tf
BC5402 484 tf
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

Warning: BC3031 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
4878 8.80e-06 CccTtCC.
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4879 3.30e+01 gGGGgAG
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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 BC3031

BC3031 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Nucleoside-diphosphate-sugar epimerases cog/ cog
catalytic activity go/ molecular_function
cellular metabolic process go/ biological_process
2'-hydroxyisoflavone reductase activity go/ molecular_function
coenzyme binding go/ molecular_function
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for BC3031

BC3031 has total of 42 gene neighbors in modules 484, 512
Gene neighbors (42)
Gene Common Name Description Module membership
BC0058 BC0058 Transcription-repair coupling factor (NCBI ptt file) 240, 484
BC0113 BC0113 hypothetical Cytosolic Protein (NCBI ptt file) 357, 484
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
BC1575 BC1575 hypothetical protein (NCBI ptt file) 179, 484
BC2341 BC2341 None 98, 484
BC2453 BC2453 Peptide synthetase (NCBI ptt file) 484, 490
BC2454 BC2454 Peptide synthetase (NCBI ptt file) 232, 484
BC2455 BC2455 Peptide synthetase (NCBI ptt file) 347, 484
BC2832 BC2832 Aldehyde dehydrogenase (NCBI ptt file) 202, 484
BC2833 BC2833 Dihydrodipicolinate synthase (NCBI ptt file) 202, 484
BC3004 BC3004 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 347, 484
BC3031 BC3031 Isoflavone reductase (NCBI ptt file) 484, 512
BC3166 BC3166 Xanthine dehydrogenase iron-sulfur subunit (NCBI ptt file) 407, 484
BC3211 BC3211 NADPH-cytochrome P450 reductase (NCBI ptt file) 484, 506
BC3346 BC3346 Collagen-like triple helix repeat protein (NCBI ptt file) 359, 512
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
BC4318 BC4318 hypothetical protein (NCBI ptt file) 202, 484
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
BC4901 BC4901 Aromatic amino acid aminotransferase (NCBI ptt file) 484, 518
BC5022 BC5022 Cytolysin immunity CylI (NCBI ptt file) 48, 484
BC5023 BC5023 hypothetical protein (NCBI ptt file) 48, 484
BC5024 BC5024 Transcriptional regulator, PBSX family (NCBI ptt file) 48, 484
BC5294 BC5294 NADH-quinone oxidoreductase chain K (NCBI ptt file) 321, 484
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 BC3031
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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