Organism : Bacillus cereus ATCC14579 | Module List :
BC4411

Queuine tRNA-ribosyltransferase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Queuine/archaeosine tRNA-ribosyltransferase cog/ cog
queuine tRNA-ribosyltransferase activity go/ molecular_function
queuosine biosynthetic process go/ biological_process
Q_tRNA_tgt tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4411
(Mouseover regulator name to see its description)

BC4411 is regulated by 23 influences and regulates 0 modules.
Regulators for BC4411 (23)
Regulator Module Operator
BC0116 66 tf
BC0122 66 tf
BC1080 66 tf
BC2410 66 tf
BC2672 66 tf
BC2773 66 tf
BC3982 66 tf
BC4010 66 tf
BC4057 66 tf
BC4356 66 tf
BC5339 66 tf
BC0122 79 tf
BC1489 79 tf
BC1998 79 tf
BC2410 79 tf
BC3320 79 tf
BC3868 79 tf
BC3982 79 tf
BC4057 79 tf
BC4525 79 tf
BC4672 79 tf
BC5339 79 tf
BC5368 79 tf

Warning: BC4411 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
4052 2.60e+02 TataAgagGGaG.g
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4053 1.80e+03 cAGAAG
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4078 5.40e+01 AtttTAgGG.g
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4079 9.00e+02 cAtcactTttTcc.T
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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 BC4411

BC4411 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Queuine/archaeosine tRNA-ribosyltransferase cog/ cog
queuine tRNA-ribosyltransferase activity go/ molecular_function
queuosine biosynthetic process go/ biological_process
Q_tRNA_tgt tigr/ tigrfam
Module neighborhood information for BC4411

BC4411 has total of 22 gene neighbors in modules 66, 79
Gene neighbors (22)
Gene Common Name Description Module membership
BC0005 BC0005 DNA gyrase subunit B (NCBI ptt file) 79, 374
BC0591 BC0591 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 79, 319
BC1354 BC1354 Ribonucleoside-diphosphate reductase alpha chain (NCBI ptt file) 66, 319
BC1355 BC1355 Ribonucleoside-diphosphate reductase beta chain (NCBI ptt file) 66, 145
BC1383 BC1383 Na+ driven multidrug efflux pump (NCBI ptt file) 66, 79
BC2180 BC2180 hypothetical protein (NCBI ptt file) 6, 79
BC3542 BC3542 Transcriptional regulator (NCBI ptt file) 66, 236
BC4045 BC4045 NAD(P)H nitroreductase (NCBI ptt file) 79, 482
BC4103 BC4103 transport protein (NCBI ptt file) 79, 201
BC4249 BC4249 UDP-N-acetylglucosamine--N-acetylmuramyl-(Pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) 27, 66
BC4403 BC4403 Single-stranded-DNA-specific exonuclease recJ (NCBI ptt file) 79, 367
BC4411 BC4411 Queuine tRNA-ribosyltransferase (NCBI ptt file) 66, 79
BC4412 BC4412 S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI ptt file) 79, 99
BC4413 BC4413 hypothetical Membrane Spanning Protein (NCBI ptt file) 79, 99
BC4414 BC4414 Holliday junction DNA helicase ruvB (NCBI ptt file) 79, 99
BC4704 BC4704 Ribosomal small subunit pseudouridine synthase A (NCBI ptt file) 66, 423
BC4705 BC4705 Export protein for polysaccharides and teichoic acids (NCBI ptt file) 66, 423
BC4707 BC4707 Multidrug resistance protein B (NCBI ptt file) 79, 527
BC5427 BC5427 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 79, 170
BC5431 BC5431 Multidrug resistance protein B (NCBI ptt file) 79, 201
BC5433 BC5433 ABC transporter ATP-binding protein uup (NCBI ptt file) 66, 319
BC5454 BC5454 Molybdenum cofactor biosynthesis enzyme and related Fe-S oxidoreductases (NCBI ptt file) 66, 236
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 BC4411
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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