Organism : Bacillus cereus ATCC14579 | Module List :
BC2166

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 BC2166
(Mouseover regulator name to see its description)

BC2166 is regulated by 24 influences and regulates 9 modules.
Regulators for BC2166 (24)
Regulator Module Operator
BC0433 369 tf
BC0690 369 tf
BC1037 369 tf
BC1053 369 tf
BC1113 369 tf
BC1715 369 tf
BC1756 369 tf
BC1814 369 tf
BC2936 369 tf
BC4206 369 tf
BC4212 369 tf
BC0051 426 tf
BC1282 426 tf
BC1477 426 tf
BC2166 426 tf
BC2434 426 tf
BC3522 426 tf
BC3976 426 tf
BC4603 426 tf
BC4670 426 tf
BC5176 426 tf
BC5205 426 tf
BC5339 426 tf
BC5373 426 tf

Warning: BC2166 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
4648 3.80e-01 TTcCaatccTAAcgatAaaGAgGG
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4649 1.80e-02 CaTTgcaACGc
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4762 5.50e+00 AGgAGG
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4763 6.10e+03 GCCaCcTCC
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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 BC2166

BC2166 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC2166

BC2166 has total of 35 gene neighbors in modules 369, 426
Gene neighbors (35)
Gene Common Name Description Module membership
BC0446 BC0446 hypothetical tellurium resistance protein (NCBI ptt file) 118, 426
BC0684 BC0684 Di-/tripeptide transporter (NCBI ptt file) 169, 426
BC0691 BC0691 hypothetical protein (NCBI ptt file) 276, 369
BC0852 BC0852 Quaternary ammonium compound-resistance protein (NCBI ptt file) 369, 498
BC1053 BC1053 Transcriptional regulator, TetR family (NCBI ptt file) 18, 369
BC1054 BC1054 hypothetical protein (NCBI ptt file) 18, 369
BC1055 BC1055 hypothetical Membrane Spanning Protein (NCBI ptt file) 315, 369
BC1056 BC1056 hypothetical Membrane Spanning Protein (NCBI ptt file) 315, 369
BC1057 BC1057 hypothetical protein (NCBI ptt file) 315, 369
BC1530 BC1530 hypothetical Membrane Spanning Protein (NCBI ptt file) 235, 426
BC1715 BC1715 Transcriptional regulator (NCBI ptt file) 369, 517
BC1716 BC1716 Na+ driven multidrug efflux pump (NCBI ptt file) 369, 517
BC2165 BC2165 hypothetical Membrane Spanning Protein (NCBI ptt file) 369, 485
BC2166 BC2166 Transcriptional regulator, TetR family (NCBI ptt file) 369, 426
BC2828 BC2828 Acetyltransferase (NCBI ptt file) 90, 426
BC2881 BC2881 hypothetical Cytosolic Protein (NCBI ptt file) 161, 369
BC2882 BC2882 hypothetical Cytosolic Protein (NCBI ptt file) 60, 369
BC2883 BC2883 hypothetical Cytosolic Protein (NCBI ptt file) 369, 485
BC2936 BC2936 Transcriptional repressor Bm3R1 (NCBI ptt file) 18, 369
BC2938 BC2938 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file) 51, 426
BC3798 BC3798 Aspartokinase (NCBI ptt file) 371, 426
BC3799 BC3799 Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 371, 426
BC3873 BC3873 Fibronectin-binding protein / Fibrinogen-binding protein (NCBI ptt file) 406, 426
BC3896 BC3896 Cell division protein DIVIVA (NCBI ptt file) 406, 426
BC4205 BC4205 Spore photoproduct lyase (NCBI ptt file) 223, 369
BC4206 BC4206 Transcriptional regulator, PadR family (NCBI ptt file) 369, 485
BC4207 BC4207 hypothetical protein (NCBI ptt file) 369, 485
BC4212 BC4212 Transcriptional regulator, TetR family (NCBI ptt file) 18, 369
BC4213 BC4213 Quaternary ammonium compound-resistance protein (NCBI ptt file) 18, 369
BC4214 BC4214 Quaternary ammonium compound-resistance protein (NCBI ptt file) 18, 369
BC4215 BC4215 hypothetical protein (NCBI ptt file) 18, 369
BC4333 BC4333 putative lipase (NCBI ptt file) 275, 426
BC4406 BC4406 hypothetical protein (NCBI ptt file) 406, 426
BC5189 BC5189 Protein translocase subunit SecA (NCBI ptt file) 70, 426
BC5257 BC5257 hypothetical protein (NCBI ptt file) 155, 369
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 BC2166
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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