Organism : Bacillus cereus ATCC14579 | Module List :
BC5200

Transcriptional regulator, LytR family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Transcriptional regulator cog/ cog
lytR_cpsA_psr tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5200
(Mouseover regulator name to see its description)

BC5200 is regulated by 24 influences and regulates 15 modules.
Regulators for BC5200 (24)
Regulator Module Operator
BC0607 442 tf
BC0801 442 tf
BC1033 442 tf
BC1363 442 tf
BC1889 442 tf
BC2340 442 tf
BC2401 442 tf
BC3982 442 tf
BC4508 442 tf
BC5200 442 tf
BC5339 442 tf
BC1477 193 tf
BC1531 193 tf
BC1537 193 tf
BC2133 193 tf
BC2551 193 tf
BC2672 193 tf
BC2815 193 tf
BC3756 193 tf
BC4277 193 tf
BC4525 193 tf
BC4842 193 tf
BC4968 193 tf
BC5200 193 tf

Warning: BC5200 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
4302 9.40e+00 GGAgGA
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4303 3.70e+01 TttCAC.TaCccTtttTTa
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4794 9.20e+02 GGGAAaGg
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4795 7.60e+04 GCAAGG
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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 BC5200

BC5200 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Transcriptional regulator cog/ cog
lytR_cpsA_psr tigr/ tigrfam
Module neighborhood information for BC5200

BC5200 has total of 37 gene neighbors in modules 193, 442
Gene neighbors (37)
Gene Common Name Description Module membership
BC0682 BC0682 Sortase (NCBI ptt file) 148, 442
BC0801 BC0801 Transcriptional regulator, LytR family (NCBI ptt file) 442, 465
BC0897 BC0897 hypothetical protein (NCBI ptt file) 159, 442
BC0921 BC0921 hypothetical protein (NCBI ptt file) 6, 442
BC1043 BC1043 Protein export protein prsA precursor (NCBI ptt file) 6, 442
BC1196 BC1196 hypothetical Cytosolic Protein (NCBI ptt file) 37, 442
BC1215 BC1215 dTDP-4-dehydrorhamnose reductase (NCBI ptt file) 193, 240
BC1242 BC1242 Integral membrane protein (NCBI ptt file) 442, 465
BC1478 BC1478 Sensor protein resE (NCBI ptt file) 193, 263
BC1734 BC1734 Export ABC transporter ATP-binding protein (NCBI ptt file) 135, 193
BC1775 BC1775 None 97, 442
BC1951 BC1951 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 159, 442
BC1953 BC1953 Enterotoxin (NCBI ptt file) 343, 442
BC2117 BC2117 MoxR protein (NCBI ptt file) 179, 193
BC2150 BC2150 metal-dependent phosphohydrolase (NCBI ptt file) 193, 417
BC2151 BC2151 ABC transporter ATP-binding protein uup (NCBI ptt file) 193, 417
BC2193 BC2193 MecA protein (NCBI ptt file) 193, 221
BC2294 BC2294 hypothetical Cytosolic Protein (NCBI ptt file) 193, 228
BC2295 BC2295 Exonuclease SbcD (NCBI ptt file) 41, 193
BC2296 BC2296 Exonuclease SbcC (NCBI ptt file) 141, 193
BC2418 BC2418 hypothetical protein (NCBI ptt file) 148, 442
BC2923 BC2923 Acetyltransferase (NCBI ptt file) 193, 453
BC3756 BC3756 Transcriptional regulator, GntR family (NCBI ptt file) 193, 449
BC3768 BC3768 DNA mismatch repair protein mutL (NCBI ptt file) 193, 367
BC3769 BC3769 DNA mismatch repair protein mutS (NCBI ptt file) 118, 193
BC3858 BC3858 Ribulose-phosphate 3-epimerase (NCBI ptt file) 270, 442
BC3975 BC3975 hydrolase (HAD superfamily) (NCBI ptt file) 148, 442
BC4020 BC4020 hypothetical protein (NCBI ptt file) 148, 442
BC4042 BC4042 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) 193, 218
BC4302 BC4302 PhoH protein (NCBI ptt file) 193, 417
BC4488 BC4488 hypothetical protein (NCBI ptt file) 37, 442
BC4540 BC4540 hypothetical protein (NCBI ptt file) 442, 477
BC4686 BC4686 Cell division protein ftsK (NCBI ptt file) 193, 451
BC5200 BC5200 Transcriptional regulator, LytR family (NCBI ptt file) 193, 442
BC5245 BC5245 SWF/SNF family helicase (NCBI ptt file) 193, 243
BC5287 BC5287 Stage II sporulation protein D (NCBI ptt file) 193, 449
BC5423 BC5423 hypothetical Membrane Spanning Protein (NCBI ptt file) 304, 442
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 BC5200
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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