Organism : Bacillus cereus ATCC14579 | Module List :
BC4222

Transcriptional regulator, GntR family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4222
(Mouseover regulator name to see its description)

BC4222 is regulated by 27 influences and regulates 22 modules.
Regulators for BC4222 (27)
Regulator Module Operator
BC0356 83 tf
BC0435 83 tf
BC0586 83 tf
BC0953 83 tf
BC1131 83 tf
BC1673 83 tf
BC1996 83 tf
BC2250 83 tf
BC2340 83 tf
BC2903 83 tf
BC3069 83 tf
BC4204 83 tf
BC4222 83 tf
BC4902 83 tf
BC5339 83 tf
BC0586 411 tf
BC1059 411 tf
BC1477 411 tf
BC1698 411 tf
BC1884 411 tf
BC2903 411 tf
BC3449 411 tf
BC3588 411 tf
BC3904 411 tf
BC3961 411 tf
BC4222 411 tf
BC4672 411 tf

Warning: BC4222 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
4084 3.80e+02 AgACgAtgtgtTaccgcGg
Loader icon
4085 1.70e+03 gGgGGAa
Loader icon
4732 3.80e+03 gaAggAgaaA.ag
Loader icon
4733 1.70e+04 GGcGTGAA
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 BC4222

BC4222 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4222

BC4222 has total of 42 gene neighbors in modules 83, 411
Gene neighbors (42)
Gene Common Name Description Module membership
BC0343 BC0343 hypothetical Membrane Spanning Protein (NCBI ptt file) 411, 436
BC0375 BC0375 Methyltransferase (NCBI ptt file) 310, 411
BC1232 BC1232 Anthranilate synthase component I (NCBI ptt file) 83, 412
BC1233 BC1233 Anthranilate synthase component II (NCBI ptt file) 83, 297
BC1234 BC1234 Anthranilate phosphoribosyltransferase (NCBI ptt file) 83, 297
BC1235 BC1235 Indole-3-glycerol phosphate synthase (NCBI ptt file) 83, 297
BC1236 BC1236 N-(5'-phosphoribosyl)anthranilate isomerase (NCBI ptt file) 83, 297
BC1237 BC1237 Tryptophan synthase beta chain (NCBI ptt file) 83, 297
BC1238 BC1238 Tryptophan synthase alpha chain (NCBI ptt file) 83, 297
BC1267 BC1267 hypothetical protein (NCBI ptt file) 4, 411
BC1271 BC1271 hypothetical protein (NCBI ptt file) 238, 411
BC1517 BC1517 3-dehydroquinate synthase (NCBI ptt file) 83, 524
BC1522 BC1522 Menaquinol-cytochrome c reductase iron-sulfur subunit (NCBI ptt file) 83, 524
BC1629 BC1629 Chemotaxis protein cheC (NCBI ptt file) 50, 83
BC1630 BC1630 hypothetical protein (NCBI ptt file) 50, 83
BC1690 BC1690 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 132, 411
BC1875 BC1875 Phage protein (NCBI ptt file) 342, 411
BC2335 BC2335 Catabolite gene activator (NCBI ptt file) 153, 411
BC2903 BC2903 Transcriptional regulator, GntR family (NCBI ptt file) 411, 498
BC3013 BC3013 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 411, 435
BC3063 BC3063 Pyrrolidone-carboxylate peptidase (NCBI ptt file) 83, 282
BC3065 BC3065 Permease (NCBI ptt file) 83, 140
BC3258 BC3258 hypothetical Cytosolic Protein (NCBI ptt file) 411, 435
BC3260 BC3260 hypothetical protein (NCBI ptt file) 114, 411
BC3266 BC3266 hypothetical protein (NCBI ptt file) 392, 411
BC3267 BC3267 hypothetical protein (NCBI ptt file) 404, 411
BC3268 BC3268 Syd protein (NCBI ptt file) 404, 411
BC3270 BC3270 hypothetical Membrane Spanning Protein (NCBI ptt file) 411, 435
BC3288 BC3288 hypothetical Cytosolic Protein (NCBI ptt file) 114, 411
BC4220 BC4220 ABC transporter permease protein (NCBI ptt file) 83, 411
BC4221 BC4221 ABC transporter ATP-binding protein (NCBI ptt file) 83, 150
BC4222 BC4222 Transcriptional regulator, GntR family (NCBI ptt file) 83, 411
BC4534 BC4534 hypothetical protein (NCBI ptt file) 310, 411
BC4699 BC4699 None 3, 83
BC5079 BC5079 Short chain dehydrogenase (NCBI ptt file) 83, 150
BC5080 BC5080 Methyltransferase (NCBI ptt file) 83, 522
BC5081 BC5081 NADH oxidase (NOXASE) (NCBI ptt file) 83, 96
BC5082 BC5082 hypothetical protein (NCBI ptt file) 83, 525
BC5083 BC5083 Lantibiotic biosynthesis protein (NCBI ptt file) 83, 525
BC5084 BC5084 Lanthionine biosynthesis protein (NCBI ptt file) 83, 525
BC5085 BC5085 hypothetical Cytosolic Protein (NCBI ptt file) 83, 525
BC5286 BC5286 Transcriptional regulator with ABC transporter ATP-binding domain and LytTR DNA-binding domain (NCBI ptt file) 411, 454
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 BC4222
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