Organism : Bacillus cereus ATCC14579 | Module List :
BC2680

Transcriptional regulator, GntR family (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2680
(Mouseover regulator name to see its description)

BC2680 is regulated by 16 influences and regulates 21 modules.
Regulators for BC2680 (16)
Regulator Module Operator
BC0566 397 tf
BC0848 397 tf
BC2410 397 tf
BC2680 397 tf
BC2837 397 tf
BC2964 397 tf
BC3095 397 tf
BC4499 397 tf
BC5205 397 tf
BC1059 131 tf
BC2517 131 tf
BC2680 131 tf
BC2837 131 tf
BC3589 131 tf
BC3903 131 tf
BC5251 131 tf

Warning: BC2680 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
4178 1.20e+02 taagGgGaGAa
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4179 1.80e+03 gt.caaCcA.a.G..G.aGtTgT
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4704 2.50e-04 GAAAgGgG
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4705 4.20e+03 AGGAGGCT
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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 BC2680

BC2680 is enriched for 7 functions in 3 categories.
Module neighborhood information for BC2680

BC2680 has total of 45 gene neighbors in modules 131, 397
Gene neighbors (45)
Gene Common Name Description Module membership
BC0255 BC0255 Amino acid permease (NCBI ptt file) 131, 384
BC0489 BC0489 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 131, 376
BC0490 BC0490 hypothetical protein (NCBI ptt file) 131, 376
BC0634 BC0634 Spore germination protein KB (NCBI ptt file) 52, 397
BC0701 BC0701 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 131, 135
BC0783 BC0783 Spore germination protein, gerC family (NCBI ptt file) 25, 131
BC0784 BC0784 Spore germination protein, gerA family (NCBI ptt file) 131, 162
BC0877 BC0877 IG hypothetical 16724 (NCBI ptt file) 46, 397
BC1153 BC1153 Asparagine synthetase (NCBI ptt file) 397, 504
BC1204 BC1204 Glycosyltransferase (NCBI ptt file) 76, 397
BC1205 BC1205 Methyltransferase (NCBI ptt file) 25, 397
BC1272 BC1272 DNA integration/recombination/invertion protein (NCBI ptt file) 397, 487
BC1538 BC1538 hypothetical protein (NCBI ptt file) 131, 521
BC1555 BC1555 hypothetical protein (NCBI ptt file) 131, 376
BC1748 BC1748 Aspartokinase (NCBI ptt file) 330, 397
BC1778 BC1778 None 89, 397
BC1942 BC1942 hypothetical protein (NCBI ptt file) 128, 131
BC2116 BC2116 None 280, 397
BC2203 BC2203 Small heat shock protein (NCBI ptt file) 250, 397
BC2325 BC2325 Macrolide-efflux protein (NCBI ptt file) 131, 280
BC2433 BC2433 Indole-3-pyruvate decarboxylase (NCBI ptt file) 299, 397
BC2577 BC2577 Phage protein (NCBI ptt file) 104, 397
BC2590 BC2590 Phage protein (NCBI ptt file) 25, 131
BC2680 BC2680 Transcriptional regulator, GntR family (NCBI ptt file) 131, 397
BC2790 BC2790 Glycine betaine transport system permease protein (NCBI ptt file) 397, 504
BC2953 BC2953 hypothetical protein (NCBI ptt file) 168, 397
BC2972 BC2972 hypothetical protein (NCBI ptt file) 339, 397
BC3059 BC3059 putative cephalosporin hydroxylase CmcI (NCBI ptt file) 131, 463
BC3092 BC3092 Glutathione-dependent formaldehyde dehydrogenase (NCBI ptt file) 128, 131
BC3327 BC3327 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 131, 301
BC3403 BC3403 hypothetical protein (NCBI ptt file) 131, 459
BC3557 BC3557 Squalene--hopene cyclase (NCBI ptt file) 76, 397
BC3583 BC3583 Methyltransferase (NCBI ptt file) 54, 397
BC3715 BC3715 hypothetical protein (NCBI ptt file) 225, 397
BC3928 BC3928 hypothetical Membrane Spanning Protein (NCBI ptt file) 131, 339
BC4044 BC4044 Sensory box/GGDEF family protein (NCBI ptt file) 25, 397
BC4070 BC4070 Stage V sporulation protein AA (NCBI ptt file) 131, 334
BC4191 BC4191 Stage III sporulation protein AC (NCBI ptt file) 131, 162
BC4527 BC4527 hypothetical Membrane Spanning Protein (NCBI ptt file) 25, 131
BC4750 BC4750 Aspartate racemase (NCBI ptt file) 370, 397
BC4868 BC4868 Cell envelope-bound metalloprotease (camelysin) (NCBI ptt file) 397, 415
BC4916 BC4916 hypothetical Cytosolic Protein (NCBI ptt file) 186, 397
BC4943 BC4943 hypothetical protein (NCBI ptt file) 131, 509
BC5316 BC5316 Serine hydroxymethyltransferase (NCBI ptt file) 397, 415
BC5480 BC5480 hypothetical protein (NCBI ptt file) 131, 272
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 BC2680
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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