Organism : Bacillus cereus ATCC14579 | Module List :
BC0355

4-aminobutyrate aminotransferase (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
4-aminobutyrate aminotransferase and related aminotransferases cog/ cog
4-aminobutyrate transaminase activity go/ molecular_function
gamma-aminobutyric acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GABAtrnsam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0355
(Mouseover regulator name to see its description)

BC0355 is regulated by 24 influences and regulates 0 modules.
Regulators for BC0355 (24)
Regulator Module Operator
BC0840 464 tf
BC1059 464 tf
BC1335 464 tf
BC1814 464 tf
BC2964 464 tf
BC3155 464 tf
BC3486 464 tf
BC3588 464 tf
BC3792 464 tf
BC3903 464 tf
BC3904 464 tf
BC4336 464 tf
BC4832 464 tf
BC4930 464 tf
BC5250 464 tf
BC0742 135 tf
BC1059 135 tf
BC1710 135 tf
BC2469 135 tf
BC2517 135 tf
BC3539 135 tf
BC4222 135 tf
BC4256 135 tf
BC5402 135 tf

Warning: BC0355 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
4186 8.60e+00 cata.tgagGaggGaaAA
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4187 3.70e+03 cgCATgCCAAA
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4838 1.10e+04 ggggataaAtagAtggTCG
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4839 1.00e+02 tTataaggagg
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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 BC0355

BC0355 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
4-aminobutyrate aminotransferase and related aminotransferases cog/ cog
4-aminobutyrate transaminase activity go/ molecular_function
gamma-aminobutyric acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GABAtrnsam tigr/ tigrfam
Module neighborhood information for BC0355

BC0355 has total of 48 gene neighbors in modules 135, 464
Gene neighbors (48)
Gene Common Name Description Module membership
BC0227 BC0227 hypothetical protein (NCBI ptt file) 464, 525
BC0355 BC0355 4-aminobutyrate aminotransferase (NCBI ptt file) 135, 464
BC0406 BC0406 Arginine deiminase (NCBI ptt file) 250, 464
BC0407 BC0407 Ornithine carbamoyltransferase (NCBI ptt file) 189, 464
BC0465 BC0465 hypothetical protein (NCBI ptt file) 391, 464
BC0485 BC0485 hypothetical protein (NCBI ptt file) 317, 464
BC0701 BC0701 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 131, 135
BC0702 BC0702 hypothetical protein (NCBI ptt file) 135, 463
BC0705 BC0705 Spore germination protein LB (NCBI ptt file) 38, 135
BC1012 BC1012 hypothetical protein (NCBI ptt file) 356, 464
BC1162 BC1162 hypothetical protein (NCBI ptt file) 17, 464
BC1208 BC1208 Beta 1,4 glucosyltransferase (NCBI ptt file) 135, 356
BC1657 BC1657 Flagellin (NCBI ptt file) 149, 464
BC1734 BC1734 Export ABC transporter ATP-binding protein (NCBI ptt file) 135, 193
BC1735 BC1735 Export ABC transporter permease protein (NCBI ptt file) 135, 502
BC1816 BC1816 hypothetical protein (NCBI ptt file) 391, 464
BC2077 BC2077 hypothetical protein (NCBI ptt file) 316, 464
BC2282 BC2282 hypothetical protein (NCBI ptt file) 135, 186
BC2283 BC2283 Quinolone resistence NorA protein (NCBI ptt file) 135, 487
BC2284 BC2284 hypothetical Cytosolic Protein (NCBI ptt file) 21, 135
BC2365 BC2365 Choloylglycine hydrolase (NCBI ptt file) 464, 502
BC2419 BC2419 Phage protein (NCBI ptt file) 184, 464
BC2421 BC2421 DNA integration/recombination/invertion protein (NCBI ptt file) 316, 464
BC2466 BC2466 Microbial collagenase (NCBI ptt file) 114, 464
BC2487 BC2487 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 138, 464
BC2562 BC2562 Phage protein (NCBI ptt file) 184, 464
BC2563 BC2563 Phage replication protein (NCBI ptt file) 184, 464
BC2565 BC2565 Phage protein (NCBI ptt file) 184, 464
BC3083 BC3083 Phage infection protein (NCBI ptt file) 46, 135
BC3134 BC3134 hypothetical protein (NCBI ptt file) 135, 376
BC3381 BC3381 hypothetical protein (NCBI ptt file) 196, 464
BC3393 BC3393 Chloramphenicol resistance protein (NCBI ptt file) 135, 205
BC3872 BC3872 None 135, 519
BC4116 BC4116 BioH protein (NCBI ptt file) 135, 202
BC4117 BC4117 8-amino-7-oxononanoate synthase (NCBI ptt file) 135, 202
BC4118 BC4118 Dethiobiotin synthetase (NCBI ptt file) 135, 202
BC4119 BC4119 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file) 135, 202
BC4235 BC4235 ComG operon protein 6 (NCBI ptt file) 135, 355
BC4238 BC4238 ComG operon protein 2 (NCBI ptt file) 135, 205
BC4239 BC4239 ComG operon protein 1 (NCBI ptt file) 135, 205
BC4447 BC4447 DNA repair protein radC (NCBI ptt file) 136, 464
BC4448 BC4448 hypothetical protein (NCBI ptt file) 434, 464
BC4449 BC4449 hypothetical Membrane Spanning Protein (NCBI ptt file) 139, 464
BC4450 BC4450 Phage integrase family protein (NCBI ptt file) 123, 464
BC4451 BC4451 hypothetical protein (NCBI ptt file) 141, 464
BC4930 BC4930 Transcriptional regulator, DeoR family (NCBI ptt file) 202, 464
BC5227 BC5227 Thiamine biosynthesis protein thiC (NCBI ptt file) 135, 424
VIMSS12791522 VIMSS12791522 None 17, 135
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 BC0355
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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