Organism : Bacillus cereus ATCC14579 | Module List :
BC0954

tcdA-E operon negative regulator (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0954
(Mouseover regulator name to see its description)

BC0954 is regulated by 27 influences and regulates 28 modules.
Regulators for BC0954 (27)
Regulator Module Operator
BC0595 410 tf
BC0613 410 tf
BC0954 410 tf
BC1841 410 tf
BC1889 410 tf
BC2340 410 tf
BC2386 410 tf
BC2434 410 tf
BC2514 410 tf
BC2526 410 tf
BC4834 410 tf
BC5256 410 tf
BC0410 213 tf
BC0595 213 tf
BC0613 213 tf
BC0648 213 tf
BC0954 213 tf
BC0975 213 tf
BC0980 213 tf
BC1296 213 tf
BC1356 213 tf
BC1622 213 tf
BC1884 213 tf
BC2794 213 tf
BC3332 213 tf
BC3961 213 tf
BC4652 213 tf

Warning: BC0954 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
4342 9.90e+02 tagAgggagatgaaa
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4343 7.50e+03 GcGcCcCC
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4730 5.80e+00 tTtatcCtCCT
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4731 2.30e+03 CaGGGG
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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 BC0954

Warning: No Functional annotations were found!

Module neighborhood information for BC0954

BC0954 has total of 49 gene neighbors in modules 213, 410
Gene neighbors (49)
Gene Common Name Description Module membership
BC0225 BC0225 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 410, 462
BC0226 BC0226 hypothetical protein (NCBI ptt file) 60, 410
BC0422 BC0422 Methyl-accepting chemotaxis protein (NCBI ptt file) 213, 462
BC0423 BC0423 Peptide synthetase (NCBI ptt file) 213, 462
BC0757 BC0757 Bicyclomycin resistance protein (NCBI ptt file) 213, 410
BC0954 BC0954 tcdA-E operon negative regulator (NCBI ptt file) 213, 410
BC0965 BC0965 hypothetical protein (NCBI ptt file) 213, 410
BC0966 BC0966 Fimbria associated protein (NCBI ptt file) 213, 410
BC0992 BC0992 hypothetical protein (NCBI ptt file) 213, 410
BC1126 BC1126 S-layer homology domain (NCBI ptt file) 213, 506
BC1309 BC1309 TerC-like protein (NCBI ptt file) 204, 410
BC2006 BC2006 Methyl-accepting chemotaxis protein (NCBI ptt file) 213, 492
BC2047 BC2047 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 213, 405
BC2184 BC2184 ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) 213, 341
BC2408 BC2408 ATP-dependent RNA helicase (NCBI ptt file) 213, 462
BC2415 BC2415 Collagen triple helix repeat protein (NCBI ptt file) 213, 241
BC2667 BC2667 DEGV protein (NCBI ptt file) 213, 462
BC2721 BC2721 Serine/threonine protein kinases (NCBI ptt file) 213, 462
BC2771 BC2771 hypothetical Exported Protein (NCBI ptt file) 62, 213
BC3122 BC3122 Arylesterase (NCBI ptt file) 213, 462
BC3180 BC3180 Low temperature requirement protein A (NCBI ptt file) 199, 410
BC3186 BC3186 hypothetical protein (NCBI ptt file) 213, 462
BC3189 BC3189 Serine transporter (NCBI ptt file) 199, 213
BC3251 BC3251 hypothetical protein (NCBI ptt file) 204, 410
BC3495 BC3495 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 199, 213
BC3505 BC3505 hypothetical protein (NCBI ptt file) 213, 266
BC3631 BC3631 Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) 199, 213
BC3874 BC3874 hypothetical protein (NCBI ptt file) 213, 462
BC4530 BC4530 hypothetical protein (NCBI ptt file) 213, 410
BC4596 BC4596 hypothetical Membrane Spanning Protein (NCBI ptt file) 213, 410
BC4999 BC4999 CAAX amino terminal protease family (NCBI ptt file) 2, 410
BC5051 BC5051 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 139, 213
BC5055 BC5055 Wall-associated protein precursor (NCBI ptt file) 213, 341
BC5065 BC5065 Methyl-accepting chemotaxis protein (NCBI ptt file) 213, 462
BC5117 BC5117 ABC transporter permease protein (NCBI ptt file) 204, 410
BC5118 BC5118 ABC transporter ATP-binding protein (NCBI ptt file) 204, 410
BC5119 BC5119 hypothetical protein (NCBI ptt file) 204, 410
BC5120 BC5120 hypothetical Cytosolic Protein (NCBI ptt file) 204, 410
BC5121 BC5121 hypothetical protein (NCBI ptt file) 204, 410
BC5122 BC5122 hypothetical Cytosolic Protein (NCBI ptt file) 204, 410
BC5123 BC5123 hypothetical protein (NCBI ptt file) 204, 410
BC5124 BC5124 hypothetical protein (NCBI ptt file) 204, 410
BC5125 BC5125 hypothetical protein (NCBI ptt file) 204, 410
BC5241 BC5241 IG hypothetical 16680 (NCBI ptt file) 204, 410
BC5243 BC5243 hypothetical protein (NCBI ptt file) 204, 410
BC5259 BC5259 ABC transporter substrate-binding protein (NCBI ptt file) 213, 283
BC5261 BC5261 Two component system histidine kinase (NCBI ptt file) 213, 283
BC5264 BC5264 EPSX protein (NCBI ptt file) 213, 462
BC5348 BC5348 None 141, 410
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 BC0954
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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