Organism : Bacillus cereus ATCC14579 | Module List :
BC3160

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 BC3160
(Mouseover regulator name to see its description)

BC3160 is regulated by 32 influences and regulates 10 modules.
Regulators for BC3160 (32)
Regulator Module Operator
BC0801 260 tf
BC0840 260 tf
BC1329 260 tf
BC1489 260 tf
BC1987 260 tf
BC2401 260 tf
BC2964 260 tf
BC3160 260 tf
BC3982 260 tf
BC5200 260 tf
BC5339 260 tf
BC5340 260 tf
BC5463 260 tf
BC0057 243 tf
BC0059 243 tf
BC0114 243 tf
BC1337 243 tf
BC1490 243 tf
BC1531 243 tf
BC2680 243 tf
BC2794 243 tf
BC3062 243 tf
BC3160 243 tf
BC3320 243 tf
BC3332 243 tf
BC3593 243 tf
BC3653 243 tf
BC3982 243 tf
BC4316 243 tf
BC4525 243 tf
BC4714 243 tf
BC5340 243 tf

Warning: BC3160 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
4402 3.90e-03 gA.aG.gAAgG
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4403 4.20e+03 GgGGGC
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4436 4.20e+03 CATccCCatCc
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4437 3.30e+01 AaGaAGaaaaggtgc
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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 BC3160

BC3160 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC3160

BC3160 has total of 39 gene neighbors in modules 243, 260
Gene neighbors (39)
Gene Common Name Description Module membership
BC0050 BC0050 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (NCBI ptt file) 260, 406
BC0056 BC0056 Peptidyl-tRNA hydrolase (NCBI ptt file) 117, 243
BC0057 BC0057 hypothetical protein (NCBI ptt file) 243, 394
BC0105 BC0105 hypothetical Membrane Associated Protein (NCBI ptt file) 22, 243
BC0254 BC0254 Homogentisate 1,2-dioxygenase (NCBI ptt file) 243, 263
BC0513 BC0513 Daunorubicin resistance ATP-binding protein drrA (NCBI ptt file) 243, 467
BC0515 BC0515 ABC transporter permease protein (NCBI ptt file) 243, 467
BC0516 BC0516 LCTB protein (NCBI ptt file) 243, 467
BC0517 BC0517 Thioredoxin-dependent thiol peroxidase (NCBI ptt file) 243, 443
BC0628 BC0628 Sensory box/GGDEF family protein (NCBI ptt file) 6, 260
BC0694 BC0694 Na+/H+ antiporter NapA (NCBI ptt file) 243, 252
BC1044 BC1044 hypothetical protein (NCBI ptt file) 6, 260
BC1184 BC1184 Na+ driven multidrug efflux pump (NCBI ptt file) 243, 527
BC1276 BC1276 hypothetical protein (NCBI ptt file) 6, 260
BC1512 BC1512 Heptaprenyl diphosphate synthase component I (NCBI ptt file) 260, 273
BC1513 BC1513 2-heptaprenyl-1,4-naphthoquinone methyltransferase (NCBI ptt file) 6, 260
BC1514 BC1514 Farnesyltransferase (NCBI ptt file) 260, 482
BC1578 BC1578 hypothetical protein (NCBI ptt file) 243, 256
BC1743 BC1743 Two-component response regulator (NCBI ptt file) 243, 252
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC2042 BC2042 putative NAD-dependent dehydrogenase (NCBI ptt file) 218, 243
BC2096 BC2096 hypothetical protein (NCBI ptt file) 148, 260
BC3160 BC3160 Transcriptional regulator, TetR family (NCBI ptt file) 243, 260
BC3471 BC3471 hypothetical protein (NCBI ptt file) 243, 306
BC3595 BC3595 Oxidoreductase (NCBI ptt file) 243, 306
BC3641 BC3641 Sensor protein atoS (NCBI ptt file) 6, 260
BC3772 BC3772 tRNA 2-methylthioadenosine synthase (NCBI ptt file) 243, 399
BC3854 BC3854 Predicted kinase related to hydroxyacetone kinase (NCBI ptt file) 260, 371
BC3930 BC3930 Methyltransferase (NCBI ptt file) 243, 260
BC3948 BC3948 Cell division protein ftsW (NCBI ptt file) 243, 260
BC3962 BC3962 Arginine decarboxylase (NCBI ptt file) 159, 260
BC4261 BC4261 hypothetical Cytosolic Protein (NCBI ptt file) 260, 406
BC4315 BC4315 Coproporphyrinogen oxidase, anaerobic (NCBI ptt file) 243, 252
BC4673 BC4673 hypothetical protein (NCBI ptt file) 243, 252
BC5097 BC5097 Leucine-responsive regulatory protein (NCBI ptt file) 260, 302
BC5196 BC5196 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 260, 390
BC5198 BC5198 DegV family protein (NCBI ptt file) 170, 260
BC5245 BC5245 SWF/SNF family helicase (NCBI ptt file) 193, 243
BC5340 BC5340 Transcriptional regulator, TetR family (NCBI ptt file) 243, 449
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 BC3160
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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