Organism : Bacillus cereus ATCC14579 | Module List :
BC0854

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 BC0854
(Mouseover regulator name to see its description)

BC0854 is regulated by 26 influences and regulates 13 modules.
Regulators for BC0854 (26)
Regulator Module Operator
BC0742 245 tf
BC0854 245 tf
BC1356 245 tf
BC1841 245 tf
BC1936 245 tf
BC2434 245 tf
BC4652 245 tf
BC4703 245 tf
BC5074 245 tf
BC5256 245 tf
BC0059 222 tf
BC0114 222 tf
BC0854 222 tf
BC1439 222 tf
BC1987 222 tf
BC2401 222 tf
BC2672 222 tf
BC3062 222 tf
BC3653 222 tf
BC3814 222 tf
BC3982 222 tf
BC4010 222 tf
BC4057 222 tf
BC4499 222 tf
BC4652 222 tf
BC5434 222 tf

Warning: BC0854 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
4360 3.30e+00 tcTctCCT
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4361 9.50e-02 AAaAAgGgaG
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4406 1.40e+02 ACaaAAaaCacatt
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4407 2.90e+03 GtAAGATtaGTGAAA
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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 BC0854

BC0854 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC0854

BC0854 has total of 43 gene neighbors in modules 222, 245
Gene neighbors (43)
Gene Common Name Description Module membership
BC0028 BC0028 SigmaK-factor processing regulatory protein BofA (NCBI ptt file) 245, 277
BC0040 BC0040 Methyltransferase (NCBI ptt file) 222, 319
BC0060 BC0060 Polysaccharides export protein (NCBI ptt file) 49, 222
BC0062 BC0062 Heat shock protein 15 (NCBI ptt file) 49, 222
BC0063 BC0063 hypothetical protein (NCBI ptt file) 49, 222
BC0064 BC0064 Spore cortex biosynthesis protein (NCBI ptt file) 222, 374
BC0287 BC0287 Glycoprotease protein family (NCBI ptt file) 245, 351
BC0497 BC0497 Cell division inhibitor (NCBI ptt file) 222, 252
BC0564 BC0564 hypothetical lipoprotein (NCBI ptt file) 245, 257
BC0636 BC0636 CAAX amino terminal protease family (NCBI ptt file) 245, 301
BC0782 BC0782 Spore germination protein, gerB family (NCBI ptt file) 96, 245
BC0828 BC0828 Alkaline phosphatase like protein (NCBI ptt file) 141, 245
BC0854 BC0854 Transcriptional regulator, TetR family (NCBI ptt file) 222, 245
BC0967 BC0967 hypothetical protein (NCBI ptt file) 108, 245
BC1434 BC1434 Na+/H+ antiporter NhaC (NCBI ptt file) 76, 222
BC1437 BC1437 Transporter yvqF (NCBI ptt file) 18, 222
BC1438 BC1438 Two-component sensor protein yvqE (NCBI ptt file) 18, 222
BC1582 BC1582 5'-3' exonuclease (NCBI ptt file) 222, 319
BC1919 BC1919 None 31, 245
BC2130 BC2130 Transporter (NCBI ptt file) 86, 245
BC2401 BC2401 Transcriptional regulator, MarR family (NCBI ptt file) 222, 256
BC2543 BC2543 ABC transporter ATP-binding protein (NCBI ptt file) 25, 245
BC2821 BC2821 Transposase (NCBI ptt file) 141, 245
BC3296 BC3296 hypothetical protein (NCBI ptt file) 241, 245
BC3523 BC3523 Hemolysin II (NCBI ptt file) 108, 245
BC3560 BC3560 hypothetical Membrane Spanning Protein (NCBI ptt file) 222, 263
BC3777 BC3777 IG hypothetical 15594 (NCBI ptt file) 62, 222
BC4056 BC4056 ComE operon protein 3 (NCBI ptt file) 62, 222
BC4346 BC4346 hypothetical Membrane Spanning Protein (NCBI ptt file) 245, 509
BC4461 BC4461 DNA repair protein radC (NCBI ptt file) 222, 242
BC4462 BC4462 Septum formation protein Maf (NCBI ptt file) 192, 222
BC4528 BC4528 Ferrichrome-binding protein (NCBI ptt file) 104, 245
BC4551 BC4551 tRNA pseudouridine synthase A (NCBI ptt file) 245, 312
BC4566 BC4566 hypothetical Membrane Spanning Protein (NCBI ptt file) 245, 421
BC4638 BC4638 Adenine-specific methyltransferase (NCBI ptt file) 62, 222
BC4751 BC4751 Sulfite reductase [NADPH] flavoprotein alpha-component (NCBI ptt file) 245, 277
BC4763 BC4763 ATP synthase protein I (NCBI ptt file) 245, 346
BC4848 BC4848 Sensor protein vanS (NCBI ptt file) 222, 449
BC5069 BC5069 hypothetical protein (NCBI ptt file) 245, 281
BC5070 BC5070 hypothetical protein (NCBI ptt file) 88, 245
BC5256 BC5256 Transcriptional regulator, PBSX family (NCBI ptt file) 103, 245
BC5434 BC5434 Transcriptional regulator, TetR family (NCBI ptt file) 222, 443
BC5458 BC5458 Protease Do (NCBI ptt file) 242, 245
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 BC0854
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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