Organism : Bacillus cereus ATCC14579 | Module List :
BC4525

Transcriptional regulator, TetR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4525
(Mouseover regulator name to see its description)

BC4525 is regulated by 25 influences and regulates 33 modules.
Regulators for BC4525 (25)
Regulator Module Operator
BC0356 112 tf
BC0598 112 tf
BC1080 112 tf
BC1427 112 tf
BC2122 112 tf
BC2178 112 tf
BC2250 112 tf
BC2770 112 tf
BC3069 112 tf
BC3493 112 tf
BC3922 112 tf
BC4104 112 tf
BC4525 112 tf
BC4672 112 tf
BC0598 328 tf
BC1531 328 tf
BC2178 328 tf
BC2217 328 tf
BC2632 328 tf
BC2770 328 tf
BC3826 328 tf
BC3922 328 tf
BC4499 328 tf
BC4525 328 tf
BC4672 328 tf

Warning: BC4525 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
4140 6.80e-01 aAgaggGG
Loader icon
4141 2.20e+04 cGGACAG
Loader icon
4570 5.40e-02 GgGGGA
Loader icon
4571 3.60e+02 G.ggcTTca.t
Loader icon
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 BC4525

BC4525 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC4525

BC4525 has total of 34 gene neighbors in modules 112, 328
Gene neighbors (34)
Gene Common Name Description Module membership
BC0450 BC0450 Protein tyrosine phosphatase (NCBI ptt file) 112, 258
BC0451 BC0451 hypothetical protein (NCBI ptt file) 112, 258
BC0621 BC0621 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file) 197, 328
BC0622 BC0622 L-threonine 3-dehydrogenase (NCBI ptt file) 197, 328
BC0898 BC0898 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 112, 395
BC1015 BC1015 Choloylglycine hydrolase (NCBI ptt file) 23, 112
BC1224 BC1224 Acetyltransferase (NCBI ptt file) 322, 328
BC1225 BC1225 2'-5' RNA ligase (NCBI ptt file) 322, 328
BC1226 BC1226 Acetyl esterase (NCBI ptt file) 194, 328
BC1507 BC1507 hypothetical protein (NCBI ptt file) 112, 525
BC2072 BC2072 Acetyltransferase (NCBI ptt file) 112, 328
BC2073 BC2073 hypothetical protein (NCBI ptt file) 112, 328
BC2917 BC2917 TPR-repeat-containing protein (NCBI ptt file) 328, 525
BC2918 BC2918 Phosphopantothenoylcysteine decarboxylase (NCBI ptt file) 112, 328
BC2919 BC2919 Aminoglycoside N3'-acetyltransferase (NCBI ptt file) 112, 328
BC3012 BC3012 Adenine deaminase (NCBI ptt file) 112, 358
BC3021 BC3021 hypothetical Cytosolic Protein (NCBI ptt file) 112, 395
BC3157 BC3157 IG hypothetical 18565 (NCBI ptt file) 112, 258
BC3994 BC3994 Exopolyphosphatase (NCBI ptt file) 112, 307
BC4023 BC4023 Acetyl-CoA acetyltransferase (NCBI ptt file) 112, 120
BC4224 BC4224 Glycine dehydrogenase [decarboxylating] (NCBI ptt file) 322, 328
BC4225 BC4225 Glycine dehydrogenase [decarboxylating] (NCBI ptt file) 322, 328
BC4226 BC4226 Aminomethyltransferase (NCBI ptt file) 322, 328
BC4516 BC4516 Succinate dehydrogenase iron-sulfur protein (NCBI ptt file) 322, 328
BC4517 BC4517 Succinate dehydrogenase flavoprotein subunit (NCBI ptt file) 322, 328
BC4518 BC4518 Succinate dehydrogenase cytochrome b558 subunit (NCBI ptt file) 322, 328
BC4522 BC4522 None 328, 434
BC4523 BC4523 Electron transfer flavoprotein beta-subunit (NCBI ptt file) 112, 328
BC4524 BC4524 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 112, 328
BC4525 BC4525 Transcriptional regulator, TetR family (NCBI ptt file) 112, 328
BC4865 BC4865 None 112, 365
BC5002 BC5002 Acyl-CoA dehydrogenase (NCBI ptt file) 112, 328
BC5003 BC5003 3-ketoacyl-CoA thiolase (NCBI ptt file) 112, 328
BC5004 BC5004 Enoyl-CoA hydratase (NCBI ptt file) 112, 328
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 BC4525
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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