Organism : Bacillus cereus ATCC14579 | Module List :
BC3522

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 BC3522
(Mouseover regulator name to see its description)

BC3522 is regulated by 32 influences and regulates 21 modules.
Regulators for BC3522 (32)
Regulator Module Operator
BC0648 436 tf
BC1059 436 tf
BC1282 436 tf
BC1335 436 tf
BC1603 436 tf
BC1698 436 tf
BC1710 436 tf
BC1884 436 tf
BC2469 436 tf
BC2903 436 tf
BC3486 436 tf
BC3522 436 tf
BC4222 436 tf
BC4336 436 tf
BC4425 436 tf
BC5251 436 tf
BC0224 172 tf
BC0648 172 tf
BC1059 172 tf
BC2801 172 tf
BC2903 172 tf
BC3400 172 tf
BC3522 172 tf
BC3961 172 tf
BC4001 172 tf
BC4029 172 tf
BC4222 172 tf
BC4336 172 tf
BC4425 172 tf
BC4650 172 tf
BC5191 172 tf
BC5363 172 tf

Warning: BC3522 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
4260 1.00e+02 AgGAGG
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4261 6.30e+03 CCGACCG
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4782 1.60e+00 AaGaGG
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4783 5.10e+03 GCCAACGC
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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 BC3522

BC3522 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC3522

BC3522 has total of 31 gene neighbors in modules 172, 436
Gene neighbors (31)
Gene Common Name Description Module membership
BC0343 BC0343 hypothetical Membrane Spanning Protein (NCBI ptt file) 411, 436
BC0366 BC0366 hypothetical protein (NCBI ptt file) 172, 310
BC0368 BC0368 hypothetical Cytosolic Protein (NCBI ptt file) 172, 436
BC0905 BC0905 Proline racemase (NCBI ptt file) 3, 436
BC0906 BC0906 Ornithine cyclodeaminase (NCBI ptt file) 3, 436
BC0955 BC0955 Phage replication protein (NCBI ptt file) 436, 519
BC1058 BC1058 hypothetical protein (NCBI ptt file) 172, 436
BC1059 BC1059 Transcriptional regulator, TetR family (NCBI ptt file) 436, 444
BC1593 BC1593 Acetyltransferase (NCBI ptt file) 114, 436
BC1721 BC1721 Cytochrome c-type biogenesis protein ccdA (NCBI ptt file) 19, 436
BC1722 BC1722 Thiol:disulfide interchange protein tlpA (NCBI ptt file) 19, 436
BC1802 BC1802 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 172, 404
BC2319 BC2319 hypothetical protein (NCBI ptt file) 172, 436
BC2441 BC2441 hypothetical protein (NCBI ptt file) 436, 456
BC2529 BC2529 Zn-dependent alcohol dehydrogenases and related dehydrogenases (NCBI ptt file) 181, 436
BC2531 BC2531 hypothetical Membrane Associated Protein (NCBI ptt file) 181, 436
BC3060 BC3060 Signal peptidase I (NCBI ptt file) 19, 172
BC3115 BC3115 Glutaminase (NCBI ptt file) 38, 436
BC3116 BC3116 Glutamine permease (NCBI ptt file) 38, 436
BC3275 BC3275 hypothetical protein (NCBI ptt file) 172, 310
BC3276 BC3276 hypothetical protein (NCBI ptt file) 60, 172
BC3522 BC3522 Transcriptional regulator, TetR family (NCBI ptt file) 172, 436
BC3677 BC3677 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 19, 436
BC4193 BC4193 Stage III sporulation protein AA (NCBI ptt file) 436, 444
BC4336 BC4336 RNA polymerase sigma-K factor (NCBI ptt file) 436, 444
BC4782 BC4782 hypothetical protein (NCBI ptt file) 172, 404
BC4820 BC4820 hypothetical protein (NCBI ptt file) 172, 223
BC4821 BC4821 hypothetical protein (NCBI ptt file) 172, 223
BC4822 BC4822 hypothetical protein (NCBI ptt file) 172, 404
BC5066 BC5066 Endonuclease/Exonuclease/phosphatase family protein (NCBI ptt file) 19, 172
BC5109 BC5109 hypothetical protein (NCBI ptt file) 436, 509
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 BC3522
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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