Organism : Bacillus cereus ATCC14579 | Module List :
BC1710

Transcriptional regulator, MerR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1710
(Mouseover regulator name to see its description)

BC1710 is regulated by 28 influences and regulates 37 modules.
Regulators for BC1710 (28)
Regulator Module Operator
BC0586 273 tf
BC0648 273 tf
BC1329 273 tf
BC1477 273 tf
BC1710 273 tf
BC1719 273 tf
BC1818 273 tf
BC2988 273 tf
BC3976 273 tf
BC4001 273 tf
BC4672 273 tf
BC5339 273 tf
BC5373 273 tf
BC0586 507 tf
BC0613 507 tf
BC0690 507 tf
BC0758 507 tf
BC1302 507 tf
BC1490 507 tf
BC1531 507 tf
BC1710 507 tf
BC2068 507 tf
BC2794 507 tf
BC4570 507 tf
BC4670 507 tf
BC5171 507 tf
BC5197 507 tf
BC5222 507 tf

Warning: BC1710 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
4462 2.30e+00 ga.AgGagggg
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4463 3.10e+04 GtCGaTGAGcC
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4924 5.60e+00 TatacGAGgGg
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4925 6.00e+03 CACCCG
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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 BC1710

BC1710 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC1710

BC1710 has total of 33 gene neighbors in modules 273, 507
Gene neighbors (33)
Gene Common Name Description Module membership
BC0043 BC0043 Methionyl-tRNA synthetase (NCBI ptt file) 273, 296
BC0071 BC0071 Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) 273, 439
BC0493 BC0493 1,2-diacylglycerol 3-glucosyltransferase (NCBI ptt file) 81, 273
BC0759 BC0759 Serine protease (NCBI ptt file) 233, 507
BC0868 BC0868 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 233, 507
BC1022 BC1022 hypothetical protein (NCBI ptt file) 122, 507
BC1194 BC1194 hypothetical Cytosolic Protein (NCBI ptt file) 40, 507
BC1195 BC1195 Globin Family Protein (NCBI ptt file) 40, 507
BC1512 BC1512 Heptaprenyl diphosphate synthase component I (NCBI ptt file) 260, 273
BC1528 BC1528 hypothetical Membrane Spanning Protein (NCBI ptt file) 261, 507
BC1710 BC1710 Transcriptional regulator, MerR family (NCBI ptt file) 273, 507
BC1719 BC1719 Transcriptional regulator, MecI family (NCBI ptt file) 15, 273
BC1818 BC1818 Transcriptional regulator, TetR family (NCBI ptt file) 6, 273
BC1826 BC1826 CcdC protein (NCBI ptt file) 118, 273
BC2044 BC2044 Magnesium and cobalt efflux protein corC (NCBI ptt file) 110, 273
BC2201 BC2201 Outer membrane protein romA (NCBI ptt file) 117, 273
BC3548 BC3548 Benzil reductase (NCBI ptt file) 233, 507
BC3605 BC3605 hypothetical Cytosolic Protein (NCBI ptt file) 438, 507
BC4089 BC4089 DNA integration/recombination/invertion protein (NCBI ptt file) 273, 447
BC4090 BC4090 hypothetical protein (NCBI ptt file) 273, 447
BC4297 BC4297 GTP-binding protein (NCBI ptt file) 273, 371
BC4321 BC4321 DNA polymerase III, delta subunit (NCBI ptt file) 41, 273
BC4570 BC4570 Transcriptional regulator, TetR family (NCBI ptt file) 268, 507
BC4633 BC4633 hypothetical Membrane Spanning Protein (NCBI ptt file) 107, 507
BC4691 BC4691 Thioredoxin (NCBI ptt file) 233, 507
BC4758 BC4758 Molybdenum cofactor biosynthesis protein B (NCBI ptt file) 119, 273
BC4936 BC4936 Diaminopimelate epimerase (NCBI ptt file) 119, 273
BC4940 BC4940 ABC transporter ATP-binding protein (NCBI ptt file) 117, 273
BC5007 BC5007 IG hypothetical 17029 (NCBI ptt file) 438, 507
BC5008 BC5008 hypothetical Cytosolic Protein (NCBI ptt file) 107, 507
BC5035 BC5035 Phenylacetic acid degradation protein paaD (NCBI ptt file) 40, 507
BC5159 BC5159 Thioredoxin reductase (NCBI ptt file) 233, 507
BC5165 BC5165 Integral membrane protein (NCBI ptt file) 74, 273
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 BC1710
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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