Organism : Bacillus cereus ATCC14579 | Module List :
BC0260

UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
UV damage repair endonuclease cog/ cog
endonuclease activity go/ molecular_function
nucleotide-excision repair go/ biological_process
uvde tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0260
(Mouseover regulator name to see its description)

BC0260 is regulated by 19 influences and regulates 0 modules.
Regulators for BC0260 (19)
Regulator Module Operator
BC0230 241 tf
BC2358 241 tf
BC2434 241 tf
BC2551 241 tf
BC2680 241 tf
BC2811 241 tf
BC4181 241 tf
BC4336 241 tf
BC5250 241 tf
BC0433 76 tf
BC0566 76 tf
BC1335 76 tf
BC1439 76 tf
BC1603 76 tf
BC4124 76 tf
BC4670 76 tf
BC4703 76 tf
BC4826 76 tf
BC5222 76 tf

Warning: BC0260 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
4072 1.50e+01 atCCtCcTc.TctaT.tatat
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4073 4.30e+03 CGCGGCG
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4398 2.50e-03 aAgGgG
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4399 3.70e+00 aAaAgGAG
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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 BC0260

BC0260 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
UV damage repair endonuclease cog/ cog
endonuclease activity go/ molecular_function
nucleotide-excision repair go/ biological_process
uvde tigr/ tigrfam
Module neighborhood information for BC0260

BC0260 has total of 62 gene neighbors in modules 76, 241
Gene neighbors (62)
Gene Common Name Description Module membership
BC0166 BC0166 hypothetical Cytosolic Protein (NCBI ptt file) 76, 462
BC0167 BC0167 Spore-specific N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 76, 462
BC0260 BC0260 UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file) 76, 241
BC0318 BC0318 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 48, 241
BC0386 BC0386 hypothetical protein (NCBI ptt file) 241, 520
BC0398 BC0398 Benzoate transport protein (NCBI ptt file) 76, 218
BC0427 BC0427 Hydroxymethylpyrimidine transport ATP-binding protein (NCBI ptt file) 104, 241
BC0480 BC0480 hypothetical protein (NCBI ptt file) 217, 241
BC0704 BC0704 None 31, 76
BC0821 BC0821 CotJC protein (NCBI ptt file) 158, 241
BC0856 BC0856 Transcriptional regulator, MarR family (NCBI ptt file) 33, 76
BC0989 BC0989 hypothetical protein (NCBI ptt file) 238, 241
BC1061 BC1061 hypothetical protein (NCBI ptt file) 59, 241
BC1170 BC1170 putative hydrolase (NCBI ptt file) 76, 407
BC1171 BC1171 Glucose epimerase (NCBI ptt file) 76, 288
BC1201 BC1201 None 76, 179
BC1204 BC1204 Glycosyltransferase (NCBI ptt file) 76, 397
BC1293 BC1293 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 76, 400
BC1356 BC1356 Transcriptional regulator, GntR family (NCBI ptt file) 75, 241
BC1362 BC1362 hypothetical protein (NCBI ptt file) 76, 288
BC1434 BC1434 Na+/H+ antiporter NhaC (NCBI ptt file) 76, 222
BC1439 BC1439 Two-component response regulator yvqC (NCBI ptt file) 76, 347
BC1450 BC1450 hypothetical protein (NCBI ptt file) 241, 504
BC1503 BC1503 hypothetical protein (NCBI ptt file) 76, 89
BC1560 BC1560 Spore coat protein D (NCBI ptt file) 84, 241
BC1631 BC1631 hypothetical protein (NCBI ptt file) 50, 76
BC1900 BC1900 None 76, 127
BC1970 BC1970 hypothetical protein (NCBI ptt file) 76, 159
BC2111 BC2111 hypothetical protein (NCBI ptt file) 241, 393
BC2212 BC2212 hypothetical protein (NCBI ptt file) 76, 517
BC2359 BC2359 CAAX amino terminal protease family (NCBI ptt file) 76, 293
BC2392 BC2392 FenI (NCBI ptt file) 241, 517
BC2404 BC2404 hypothetical Cytosolic Protein (NCBI ptt file) 217, 241
BC2415 BC2415 Collagen triple helix repeat protein (NCBI ptt file) 213, 241
BC2515 BC2515 Macrolide-efflux protein (NCBI ptt file) 241, 491
BC2555 BC2555 hypothetical protein (NCBI ptt file) 76, 468
BC2643 BC2643 hydrolase (HAD superfamily) (NCBI ptt file) 123, 241
BC2719 BC2719 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 76, 276
BC2725 BC2725 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 241, 250
BC2741 BC2741 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 76, 217
BC2838 BC2838 hypothetical protein (NCBI ptt file) 76, 218
BC3033 BC3033 Transcriptional regulator, AraC family (NCBI ptt file) 76, 468
BC3296 BC3296 hypothetical protein (NCBI ptt file) 241, 245
BC3477 BC3477 Quinone oxidoreductase (NCBI ptt file) 72, 76
BC3557 BC3557 Squalene--hopene cyclase (NCBI ptt file) 76, 397
BC3558 BC3558 Integral membrane protein (NCBI ptt file) 241, 370
BC3776 BC3776 Stage V sporulation protein S (NCBI ptt file) 76, 481
BC3801 BC3801 Dipicolinate synthase, A chain (NCBI ptt file) 76, 407
BC4281 BC4281 IG hypothetical 17696 (NCBI ptt file) 76, 288
BC4374 BC4374 Transcription elongation factor greA (NCBI ptt file) 238, 241
BC4504 BC4504 Stress-responsive transcriptional regulator PspC (NCBI ptt file) 241, 398
BC4612 BC4612 hypothetical protein (NCBI ptt file) 76, 141
BC4632 BC4632 hypothetical protein (NCBI ptt file) 220, 241
BC4651 BC4651 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 241, 415
BC4718 BC4718 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 241, 405
BC4858 BC4858 DnaK suppressor protein (NCBI ptt file) 217, 241
BC4976 BC4976 hypothetical protein (NCBI ptt file) 241, 359
BC5099 BC5099 hypothetical protein (NCBI ptt file) 76, 104
BC5181 BC5181 hypothetical protein (NCBI ptt file) 76, 77
BC5222 BC5222 Transcriptional regulators, LysR family (NCBI ptt file) 76, 96
BC5391 BC5391 hypothetical protein (NCBI ptt file) 241, 351
BC5410 BC5410 FMN-dependent NADH-azoreductase (NCBI ptt file) 76, 353
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 BC0260
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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