Organism : Bacillus cereus ATCC14579 | Module List :
BC3592

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 BC3592
(Mouseover regulator name to see its description)

BC3592 is regulated by 27 influences and regulates 12 modules.
Regulators for BC3592 (27)
Regulator Module Operator
BC0435 354 tf
BC1131 354 tf
BC1724 354 tf
BC2340 354 tf
BC2517 354 tf
BC2903 354 tf
BC2988 354 tf
BC3592 354 tf
BC3704 354 tf
BC4222 354 tf
BC4425 354 tf
BC4930 354 tf
BC0114 20 tf
BC0801 20 tf
BC1363 20 tf
BC1818 20 tf
BC1889 20 tf
BC2217 20 tf
BC2444 20 tf
BC3244 20 tf
BC3493 20 tf
BC3592 20 tf
BC3983 20 tf
BC4010 20 tf
BC4826 20 tf
BC5251 20 tf
BC5402 20 tf

Warning: BC3592 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
3962 3.10e+02 taa.gaagagGA.GAaaaaaagaa
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3963 2.40e+04 CGCCCc
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4618 4.30e-02 A.aaaGgaGt.ataa
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4619 1.00e+04 AGGAG.aTaGg
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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 BC3592

BC3592 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC3592

BC3592 has total of 58 gene neighbors in modules 20, 354
Gene neighbors (58)
Gene Common Name Description Module membership
BC0334 BC0334 Phosphoribosylamine--glycine ligase (NCBI ptt file) 313, 354
BC0349 BC0349 hypothetical protein (NCBI ptt file) 20, 163
BC0360 BC0360 Aminopeptidase (NCBI ptt file) 20, 488
BC0458 BC0458 Alkaline phosphatase like protein (NCBI ptt file) 354, 443
BC0766 BC0766 Methylthioribose transport system permease protein (NCBI ptt file) 20, 63
BC0781 BC0781 hypothetical protein (NCBI ptt file) 20, 364
BC0830 BC0830 hypothetical protein (NCBI ptt file) 86, 354
BC0986 BC0986 Response regulator aspartate phosphatase (NCBI ptt file) 20, 416
BC1133 BC1133 hypothetical protein (NCBI ptt file) 7, 354
BC1172 BC1172 ComZ protein (NCBI ptt file) 20, 477
BC1178 BC1178 hypothetical protein (NCBI ptt file) 20, 73
BC1283 BC1283 SinI protein (NCBI ptt file) 64, 354
BC1291 BC1291 Transporter, MMPL family (NCBI ptt file) 126, 354
BC1386 BC1386 hypothetical protein (NCBI ptt file) 100, 354
BC1418 BC1418 hypothetical protein (NCBI ptt file) 128, 354
BC1431 BC1431 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 20, 416
BC1609 BC1609 Sodium/proline symporter (NCBI ptt file) 134, 354
BC1624 BC1624 hydrolase (HAD superfamily) (NCBI ptt file) 20, 227
BC1724 BC1724 Transcriptional regulator, MerR family (NCBI ptt file) 354, 478
BC1769 BC1769 hypothetical protein (NCBI ptt file) 20, 26
BC1889 BC1889 Phage protein (NCBI ptt file) 20, 254
BC1976 BC1976 Membrane protein, MgtC/SapB family (NCBI ptt file) 354, 430
BC2243 BC2243 None 20, 381
BC2263 BC2263 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 100, 354
BC2364 BC2364 hypothetical protein (NCBI ptt file) 6, 20
BC2527 BC2527 CAAX amino terminal protease family (NCBI ptt file) 100, 354
BC2671 BC2671 ThiJ/PfpI family (NCBI ptt file) 20, 90
BC2675 BC2675 Acetyltransferase (NCBI ptt file) 20, 304
BC2749 BC2749 Acetyltransferase (NCBI ptt file) 20, 146
BC2750 BC2750 hypothetical protein (NCBI ptt file) 20, 279
BC2797 BC2797 Acetyltransferase (NCBI ptt file) 6, 20
BC2809 BC2809 Phosphinothricin N-acetyltransferase (NCBI ptt file) 20, 258
BC2817 BC2817 hypothetical protein (NCBI ptt file) 337, 354
BC2885 BC2885 Peptide permease (NCBI ptt file) 228, 354
BC2886 BC2886 hypothetical protein (NCBI ptt file) 41, 354
BC3421 BC3421 Transcriptional regulator, MarR family (NCBI ptt file) 20, 485
BC3460 BC3460 Short chain dehydrogenase (NCBI ptt file) 20, 478
BC3518 BC3518 Response regulator aspartate phosphatase (NCBI ptt file) 20, 163
BC3592 BC3592 Transcriptional regulator, TetR family (NCBI ptt file) 20, 354
BC3713 BC3713 Hfq protein (NCBI ptt file) 64, 354
BC3753 BC3753 IG hypothetical 17894 (NCBI ptt file) 15, 354
BC3996 BC3996 hypothetical Exported Protein (NCBI ptt file) 20, 440
BC4035 BC4035 Aspartate aminotransferase (NCBI ptt file) 20, 408
BC4108 BC4108 hypothetical protein (NCBI ptt file) 354, 443
BC4123 BC4123 Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) 20, 343
BC4146 BC4146 Protein erfK/srfK precursor (NCBI ptt file) 20, 63
BC4408 BC4408 hypothetical Membrane Associated Protein (NCBI ptt file) 343, 354
BC4656 BC4656 hypothetical protein (NCBI ptt file) 288, 354
BC4908 BC4908 hypothetical Membrane Associated Protein (NCBI ptt file) 20, 284
BC4929 BC4929 Macrolide-efflux protein (NCBI ptt file) 20, 100
BC4931 BC4931 hypothetical Cytosolic Protein (NCBI ptt file) 20, 316
BC4941 BC4941 YbbM family integral membrane protein (NCBI ptt file) 354, 415
BC4947 BC4947 hypothetical protein (NCBI ptt file) 20, 63
BC5020 BC5020 hypothetical protein (NCBI ptt file) 221, 354
BC5046 BC5046 Lysine decarboxylase family (NCBI ptt file) 20, 284
BC5174 BC5174 hypothetical Membrane Spanning Protein (NCBI ptt file) 354, 501
BC5249 BC5249 hypothetical protein (NCBI ptt file) 354, 443
BC5349 BC5349 PapR protein (NCBI ptt file) 100, 354
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 BC3592
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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