Organism : Bacillus cereus ATCC14579 | Module List :
BC1491

NAD-specific glutamate dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Glutamate dehydrogenase/leucine dehydrogenase cog/ cog
glutamate dehydrogenase [NAD(P)+] activity go/ molecular_function
cellular amino acid metabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1491
(Mouseover regulator name to see its description)

BC1491 is regulated by 36 influences and regulates 0 modules.
Regulators for BC1491 (36)
Regulator Module Operator
BC0123 445 tf
BC0213 445 tf
BC0433 445 tf
BC0601 445 tf
BC0758 445 tf
BC0954 445 tf
BC0958 445 tf
BC1296 445 tf
BC1673 445 tf
BC1936 445 tf
BC1998 445 tf
BC2434 445 tf
BC3356 445 tf
BC3813 445 tf
BC4181 445 tf
BC5222 445 tf
BC5256 445 tf
BC5265 445 tf
BC5332 445 tf
BC0518 129 tf
BC0742 129 tf
BC1113 129 tf
BC1936 129 tf
BC2358 129 tf
BC2434 129 tf
BC3062 129 tf
BC3163 129 tf
BC3255 129 tf
BC3356 129 tf
BC3449 129 tf
BC3813 129 tf
BC3891 129 tf
BC4101 129 tf
BC4652 129 tf
BC4670 129 tf
BC4703 129 tf

Warning: BC1491 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
4174 1.10e-01 atTCCTCc
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4175 6.10e+02 CACTTGatTAGTAaA
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4800 1.30e-01 agGGAggTaTt
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4801 8.80e+00 aAa.aAgggGGAgAg
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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 BC1491

BC1491 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Glutamate dehydrogenase/leucine dehydrogenase cog/ cog
glutamate dehydrogenase [NAD(P)+] activity go/ molecular_function
cellular amino acid metabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for BC1491

BC1491 has total of 47 gene neighbors in modules 129, 445
Gene neighbors (47)
Gene Common Name Description Module membership
BC0246 BC0246 hydrolase (HAD superfamily) (NCBI ptt file) 107, 129
BC0397 BC0397 hypothetical Cytosolic Protein (NCBI ptt file) 129, 216
BC0668 BC0668 (R,R)-butanediol dehydrogenase (NCBI ptt file) 43, 445
BC0883 BC0883 Acetolactate synthase large subunit (NCBI ptt file) 43, 445
BC0884 BC0884 Alpha-acetolactate decarboxylase (NCBI ptt file) 43, 445
BC1024 BC1024 Glyoxalase family protein (NCBI ptt file) 129, 224
BC1025 BC1025 Glyoxalase family protein (NCBI ptt file) 129, 224
BC1188 BC1188 Arsenate reductase family protein (NCBI ptt file) 129, 166
BC1251 BC1251 Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex (NCBI ptt file) 43, 445
BC1252 BC1252 2-oxoglutarate dehydrogenase E1 component (NCBI ptt file) 43, 445
BC1390 BC1390 Potassium uptake protein KtrB (NCBI ptt file) 43, 445
BC1491 BC1491 NAD-specific glutamate dehydrogenase (NCBI ptt file) 129, 445
BC1602 BC1602 hypothetical Cytosolic Protein (NCBI ptt file) 129, 381
BC1936 BC1936 Transcriptional regulator, MarR family (NCBI ptt file) 70, 129
BC1937 BC1937 Luciferase-like monooxygenase (NCBI ptt file) 70, 129
BC2011 BC2011 Non-specific DNA-binding protein Dps / Iron-binding ferritin-like antioxidant protein / Ferroxidase (NCBI ptt file) 119, 129
BC2223 BC2223 Gluconokinase (NCBI ptt file) 43, 445
BC2224 BC2224 Gluconate permease (NCBI ptt file) 43, 445
BC2225 BC2225 6-phosphogluconate dehydrogenase (NCBI ptt file) 43, 445
BC2472 BC2472 None 445, 502
BC2844 BC2844 None 129, 380
BC2932 BC2932 Phosphoglycerol transferase (NCBI ptt file) 43, 445
BC3419 BC3419 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 445, 491
BC3525 BC3525 hypothetical Cytosolic Protein (NCBI ptt file) 129, 381
BC3567 BC3567 None 104, 445
BC3568 BC3568 Formate transporter (NCBI ptt file) 398, 445
BC3569 BC3569 Molybdenum cofactor biosynthesis protein A (NCBI ptt file) 43, 445
BC3570 BC3570 FdhD protein (fdsC) (NCBI ptt file) 43, 445
BC3571 BC3571 hypothetical Cytosolic Protein (NCBI ptt file) 43, 445
BC3572 BC3572 hypothetical protein (NCBI ptt file) 43, 445
BC3573 BC3573 Formate dehydrogenase alpha chain (NCBI ptt file) 43, 445
BC3818 BC3818 None 51, 445
BC3974 BC3974 Polypeptide deformylase (NCBI ptt file) 119, 129
BC4125 BC4125 hypothetical protein (NCBI ptt file) 47, 445
BC4167 BC4167 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 422
BC4625 BC4625 Universal stress protein family (NCBI ptt file) 129, 187
BC4703 BC4703 Transcriptional regulator, DeoR family (NCBI ptt file) 119, 129
BC4754 BC4754 putative acetyltransferase/acyltransferase (NCBI ptt file) 129, 422
BC4801 BC4801 Phage shock protein A (NCBI ptt file) 119, 129
BC4900 BC4900 S1-type RNA-binding domain (NCBI ptt file) 129, 227
BC4977 BC4977 5'-nucleotidase (NCBI ptt file) 105, 445
BC5016 BC5016 60 kDa inner membrane protein YIDC (NCBI ptt file) 70, 129
BC5017 BC5017 hypothetical protein (NCBI ptt file) 70, 129
BC5190 BC5190 Probable Sigma (54) modulation protein / SSU ribosomal protein S30P (NCBI ptt file) 129, 187
BC5374 BC5374 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 187
BC5445 BC5445 Superoxide dismutase [Mn] (NCBI ptt file) 43, 445
BC5459 BC5459 None 208, 445
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 BC1491
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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