Organism : Bacillus subtilis | Module List :
BSU01480 truA

tRNA pseudouridine synthase A (RefSeq)

CircVis
Functional Annotations (6)
Function System
Pseudouridylate synthase cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridylate synthase activity go/ molecular_function
pseudouridine synthase activity go/ molecular_function
hisT_truA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU01480
(Mouseover regulator name to see its description)

BSU01480 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU01480 truA (22)
Regulator Module Operator
BSU02370 176 tf
BSU04060 176 tf
BSU04100 176 tf
BSU10860 176 tf
BSU16600 176 tf
BSU24320 176 tf
BSU30020 176 tf
BSU35050 176 tf
BSU00470 374 tf
BSU01010 374 tf
BSU01080 374 tf
BSU01430 374 tf
BSU02680 374 tf
BSU03850 374 tf
BSU15970 374 tf
BSU16170 374 tf
BSU16600 374 tf
BSU16810 374 tf
BSU23210 374 tf
BSU25200 374 tf
BSU31410 374 tf
BSU36020 374 tf

Warning: BSU01480 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
5300 1.80e+02 caGGAGgc
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5301 2.20e+03 GACTGGGG
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5664 1.50e+02 AGggaGCGgGTT
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5665 2.10e+02 AAAGGG
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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 BSU01480

BSU01480 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Pseudouridylate synthase cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridylate synthase activity go/ molecular_function
pseudouridine synthase activity go/ molecular_function
hisT_truA tigr/ tigrfam
Module neighborhood information for BSU01480

BSU01480 has total of 33 gene neighbors in modules 176, 374
Gene neighbors (33)
Gene Common Name Description Module membership
BSU01450 cbiO cobalt transporter ATP-binding subunit (RefSeq) 122, 176
BSU01460 cbiO cobalt transporter ATP-binding subunit (RefSeq) 176, 374
BSU01470 ybaF putative permease (RefSeq) 30, 176
BSU01480 truA tRNA pseudouridine synthase A (RefSeq) 176, 374
BSU04050 ycsF LamB/YcsF family protein (RefSeq) 176, 240
BSU04060 ycsG putative branched chain amino acids transporter (RefSeq) 176, 240
BSU04070 ycsI hypothetical protein (RefSeq) 176, 240
BSU04080 kipI putative inhibitor of the autophosphorylation reaction of KinA (RefSeq) 176, 240
BSU04090 kipA putative hydrolase subunit antagonist of KipI (RefSeq) 176, 240
BSU04100 kipR transcriptional regulator (IclR family) (RefSeq) 176, 240
BSU06360 guaA GMP synthase (RefSeq) 79, 374
BSU09165 BSU09165 None 67, 176
BSU12671 BSU12671 None 51, 176
BSU14770 bipA GTPase (RefSeq) 212, 374
BSU15070 ylbN hypothetical protein (RefSeq) 3, 374
BSU15220 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase (RefSeq) 176, 193
BSU15990 rpsP 30S ribosomal protein S16 (RefSeq) 212, 374
BSU16590 ylxS hypothetical protein (RefSeq) 34, 374
BSU18440 gltD glutamate synthase subunit beta (RefSeq) 1, 176
BSU18450 gltA glutamate synthase (large subunit) (RefSeq) 1, 176
BSU25620 yqeL hypothetical protein (RefSeq) 204, 374
BSU25630 yqeK putative hydrolase (RefSeq) 204, 374
BSU25650 yqeI putative RNA-binding protein (RefSeq) 204, 374
BSU26075 BSU26075 None 24, 176
BSU27330 udk uridine kinase (RefSeq) 176, 227
BSU28000 minC septum formation inhibitor (RefSeq) 212, 374
BSU28850 rplT 50S ribosomal protein L20 (RefSeq) 103, 374
BSU28860 rpmI 50S ribosomal protein L35 (RefSeq) 103, 374
BSU28870 infC translation initiation factor IF-3 (RefSeq) 103, 374
BSU30550 metK S-adenosylmethionine synthetase (RefSeq) 325, 374
BSU35720 tagF CDP-glycerol:polyglycerol phosphate glycero-phosphotransferase (poly(glycerol phosphate) polymerase) (RefSeq) 204, 374
VIMSS36726 VIMSS36726 None 176, 235
VIMSS39187 VIMSS39187 None 176, 235
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 BSU01480
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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