Organism : Bacillus cereus ATCC14579 | Module List :
BC3892

Ribosomal large subunit pseudouridine synthase D (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3892
(Mouseover regulator name to see its description)

BC3892 is regulated by 28 influences and regulates 0 modules.
Regulators for BC3892 (28)
Regulator Module Operator
BC0122 133 tf
BC0595 133 tf
BC0993 133 tf
BC1841 133 tf
BC2218 133 tf
BC2770 133 tf
BC3706 133 tf
BC3826 133 tf
BC3868 133 tf
BC3922 133 tf
BC4072 133 tf
BC5265 133 tf
BC5332 133 tf
BC0116 192 tf
BC0122 192 tf
BC0607 192 tf
BC0657 192 tf
BC0680 192 tf
BC0856 192 tf
BC1841 192 tf
BC2631 192 tf
BC2672 192 tf
BC2770 192 tf
BC3062 192 tf
BC3814 192 tf
BC3826 192 tf
BC3982 192 tf
BC4010 192 tf

Warning: BC3892 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
4182 1.90e+02 atAgAtagaAGGag
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4183 1.20e+04 GGgGAA
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4300 8.00e+01 CGTGcAgtcggc
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4301 4.50e+02 gaGGtGGA
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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 BC3892

BC3892 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for BC3892

BC3892 has total of 35 gene neighbors in modules 133, 192
Gene neighbors (35)
Gene Common Name Description Module membership
BC0481 BC0481 Glutaminase (NCBI ptt file) 27, 133
BC0504 BC0504 A/G-specific adenine DNA glycosylase (NCBI ptt file) 192, 466
BC0654 BC0654 Sulfate transporter (NCBI ptt file) 192, 312
BC1341 BC1341 Aluminum resistance protein (NCBI ptt file) 192, 476
BC1342 BC1342 6-pyruvoyl tetrahydrobiopterin synthase (NCBI ptt file) 192, 476
BC1343 BC1343 Organic radical activating enzyme (NCBI ptt file) 192, 476
BC1344 BC1344 GTP cyclohydrolase I (NCBI ptt file) 192, 313
BC1432 BC1432 Proton/sodium-glutamate symport protein (NCBI ptt file) 133, 337
BC1553 BC1553 Multimodular transpeptidase-transglycosylase (NCBI ptt file) 176, 192
BC1793 BC1793 Chlorohydrolase/deaminase family protein (NCBI ptt file) 92, 133
BC2021 BC2021 High-affinity zinc uptake system protein znuA precursor (NCBI ptt file) 92, 133
BC3553 BC3553 Sodium/pantothenate symporter (NCBI ptt file) 192, 312
BC3554 BC3554 Sodium/pantothenate symporter (NCBI ptt file) 177, 192
BC3705 BC3705 None 133, 142
BC3706 BC3706 Transcriptional regulator, MerR family (NCBI ptt file) 133, 142
BC3765 BC3765 Phosphoglycerol transferase (NCBI ptt file) 133, 382
BC3831 BC3831 DNA topoisomerase I (NCBI ptt file) 192, 399
BC3892 BC3892 Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) 133, 192
BC3893 lspA lipoprotein signal peptidase (RefSeq) 139, 192
BC4285 BC4285 None 27, 133
BC4286 BC4286 NIF3-related protein (NCBI ptt file) 161, 192
BC4287 BC4287 hypothetical Cytosolic Protein (NCBI ptt file) 161, 192
BC4444 BC4444 Rod shape-determining protein mreD (NCBI ptt file) 49, 192
BC4445 BC4445 Rod shape-determining protein mreC (NCBI ptt file) 192, 242
BC4446 BC4446 Rod shape-determining protein mreB (NCBI ptt file) 192, 242
BC4462 BC4462 Septum formation protein Maf (NCBI ptt file) 192, 222
BC4507 BC4507 Aquaporin (NCBI ptt file) 92, 133
BC4795 BC4795 hypothetical Membrane Spanning Protein (NCBI ptt file) 133, 221
BC4911 BC4911 Arsenical pump membrane protein (NCBI ptt file) 133, 236
BC5012 BC5012 Chloramphenicol resistance protein (NCBI ptt file) 92, 133
BC5235 BC5235 Nucleoside permease nupC (NCBI ptt file) 92, 133
BC5265 BC5265 Transcriptional regulator, LytR family (NCBI ptt file) 133, 396
BC5314 BC5314 hypothetical protein (NCBI ptt file) 133, 182
BC5330 BC5330 Thymidine kinase (NCBI ptt file) 133, 142
BC5389 BC5389 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 133, 204
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 BC3892
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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