Organism : Bacillus cereus ATCC14579 | Module List :
BC3039

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 BC3039
(Mouseover regulator name to see its description)

BC3039 is regulated by 14 influences and regulates 6 modules.
Regulators for BC3039 (14)
Regulator Module Operator
BC1115 250 tf
BC1253 250 tf
BC1531 250 tf
BC2410 250 tf
BC3039 250 tf
BC4336 250 tf
BC5463 250 tf
BC1710 153 tf
BC2410 153 tf
BC2469 153 tf
BC3039 153 tf
BC3587 153 tf
BC3904 153 tf
BC5251 153 tf

Warning: BC3039 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
4222 9.50e-04 AAatag.aaaGggGagATt.t
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4223 2.70e+00 cCtCC.cATcTcTTAT
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4416 1.90e-02 aGGAGg
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4417 4.70e+04 CCCCtTaCC
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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 BC3039

BC3039 is enriched for 7 functions in 3 categories.
Module neighborhood information for BC3039

BC3039 has total of 39 gene neighbors in modules 153, 250
Gene neighbors (39)
Gene Common Name Description Module membership
BC0406 BC0406 Arginine deiminase (NCBI ptt file) 250, 464
BC0408 BC0408 Arginine/ornithine antiporter (NCBI ptt file) 250, 294
BC0409 BC0409 Carbamate kinase (NCBI ptt file) 250, 294
BC0580 BC0580 NAD-dependent malic enzyme (NCBI ptt file) 234, 250
BC0825 BC0825 hypothetical protein (NCBI ptt file) 250, 446
BC0971 BC0971 Carboxylic ester hydrolase (NCBI ptt file) 250, 468
BC0983 BC0983 hypothetical protein (NCBI ptt file) 153, 454
BC1723 BC1723 Prolipoprotein diacylglyceryl transferase (NCBI ptt file) 30, 250
BC1822 BC1822 pyrimidine-nucleoside phosphorylase (RefSeq) 250, 401
BC1823 BC1823 Cytidine deaminase (NCBI ptt file) 199, 250
BC2016 BC2016 Amine oxidase [flavin-containing] (NCBI ptt file) 153, 168
BC2203 BC2203 Small heat shock protein (NCBI ptt file) 250, 397
BC2227 BC2227 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 104, 153
BC2228 BC2228 hypothetical protein (NCBI ptt file) 61, 153
BC2290 BC2290 Methylmalonate-semialdehyde dehydrogenase (acylating) (NCBI ptt file) 212, 250
BC2329 BC2329 Zinc uptake transporter (NCBI ptt file) 199, 250
BC2334 BC2334 hypothetical Membrane Spanning Protein (NCBI ptt file) 115, 153
BC2335 BC2335 Catabolite gene activator (NCBI ptt file) 153, 411
BC2384 BC2384 hypothetical protein (NCBI ptt file) 250, 294
BC2394 BC2394 PTS system, diacetylchitobiose-specific IIC component (NCBI ptt file) 108, 250
BC2528 BC2528 hypothetical protein (NCBI ptt file) 250, 293
BC2594 BC2594 Phage protein (NCBI ptt file) 111, 153
BC2595 BC2595 Gp13 protein (NCBI ptt file) 153, 376
BC2596 BC2596 Phage endopeptidase (NCBI ptt file) 153, 446
BC2597 BC2597 Phage protein (NCBI ptt file) 111, 153
BC2622 BC2622 Macrolide glycosyltransferase (NCBI ptt file) 85, 250
BC2676 BC2676 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 250, 434
BC2725 BC2725 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 241, 250
BC2888 BC2888 Integral membrane protein (NCBI ptt file) 153, 489
BC2951 BC2951 hypothetical protein (NCBI ptt file) 158, 250
BC3038 BC3038 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 153
BC3039 BC3039 Transcriptional regulator, GntR family (NCBI ptt file) 153, 250
BC3145 BC3145 hypothetical protein (NCBI ptt file) 186, 250
BC3509 BC3509 CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 31, 250
BC3564 BC3564 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 153, 267
BC3565 BC3565 Molybdopterin (MPT) converting factor, subunit 2 (NCBI ptt file) 153, 398
BC3716 BC3716 None 153, 376
BC4535 BC4535 Bacitracin transport permease protein BCRB (NCBI ptt file) 250, 256
BC5213 BC5213 Spermidine synthase (NCBI ptt file) 138, 250
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 BC3039
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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