Organism : Pseudomonas aeruginosa | Module List :
PA0933 ygcA

probable RNA methyltransferase (NCBI)

CircVis
Functional Annotations (5)
Function System
SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
rumA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0933
(Mouseover regulator name to see its description)

PA0933 is regulated by 38 influences and regulates 0 modules.
Regulators for PA0933 ygcA (38)
Regulator Module Operator
PA1422 195 tf
PA1504 195 tf
PA1526 195 tf
PA1776 195 tf
PA3285 195 tf
PA3604 195 tf
PA3804 195 tf
PA4052 195 tf
PA4275 195 tf
PA4279 195 tf
PA4451 195 tf
PA4745 195 tf
PA4769 195 tf
PA4853 195 tf
PA5239 195 tf
PA5438 195 tf
PA5550 195 tf
PA0120 451 tf
PA0149 451 tf
PA0179 451 tf
PA0547 451 tf
PA1125 451 tf
PA2577 451 tf
PA2622 451 tf
PA3002 451 tf
PA3583 451 tf
PA3778 451 tf
PA4052 451 tf
PA4070 451 tf
PA4269 451 tf
PA4275 451 tf
PA4279 451 tf
PA4451 451 tf
PA4745 451 tf
PA4853 451 tf
PA4890 451 tf
PA5550 451 tf
PA5562 451 tf

Warning: PA0933 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
3218 5.00e-03 tTcca.cGgaAAg
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3219 7.80e+03 TTTaTaCT
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3720 1.60e-12 GcTA.aaTgcgc.cCcTtTgC
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3721 2.30e+00 CtGGAccacCAtcac
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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 PA0933

PA0933 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
rumA tigr/ tigrfam
Module neighborhood information for PA0933

PA0933 has total of 35 gene neighbors in modules 195, 451
Gene neighbors (35)
Gene Common Name Description Module membership
PA0012 PA0012 hypothetical protein (NCBI) 195, 296
PA0162 PA0162 probable porin (NCBI) 315, 451
PA0317 PA0317 hypothetical protein (NCBI) 249, 451
PA0354 PA0354 hypothetical protein (NCBI) 312, 451
PA0554 PA0554 hypothetical protein (NCBI) 59, 195
PA0608 gph probable phosphoglycolate phosphatase (NCBI) 332, 451
PA0733 PA0733 probable pseudouridylate synthase (NCBI) 103, 451
PA0734 PA0734 hypothetical protein (NCBI) 103, 451
PA0758 PA0758 hypothetical protein (NCBI) 78, 195
PA0932 cysM cysteine synthase B (NCBI) 103, 195
PA0933 ygcA probable RNA methyltransferase (NCBI) 195, 451
PA1170 PA1170 hypothetical protein (NCBI) 20, 195
PA1407 PA1407 hypothetical protein (NCBI) 321, 451
PA1774 cfrX CfrX protein (NCBI) 100, 195
PA1775 cmpX conserved cytoplasmic membrane protein, CmpX protein (NCBI) 100, 195
PA1776 sigX ECF sigma factor SigX (NCBI) 57, 195
PA2798 PA2798 probable two-component response regulator (NCBI) 72, 195
PA2817 PA2817 hypothetical protein (NCBI) 86, 195
PA2959 PA2959 hypothetical protein (NCBI) 1, 195
PA2960 pilZ type 4 fimbrial biogenesis protein PilZ (NCBI) 1, 195
PA3012 PA3012 hypothetical protein (NCBI) 117, 195
PA3084 PA3084 hypothetical protein (NCBI) 94, 195
PA3134 gltX glutamyl-tRNA synthetase (NCBI) 395, 451
PA3267 PA3267 hypothetical protein (NCBI) 100, 195
PA3285 PA3285 probable sigma-70 factor, ECF subfamily (NCBI) 41, 195
PA3452 mqoA malate:quinone oxidoreductase (NCBI) 195, 549
PA4044 dxs 1-deoxy-D-xylulose-5-phosphate synthase (NCBI) 395, 451
PA4116 PA4116 hypothetical protein (NCBI) 59, 195
PA4519 speC ornithine decarboxylase (NCBI) 78, 195
PA4997 msbA transport protein MsbA (NCBI) 103, 451
PA4998 PA4998 hypothetical protein (NCBI) 451, 549
PA5036 gltB glutamate synthase large chain precursor (NCBI) 62, 451
PA5047 PA5047 hypothetical protein (NCBI) 195, 296
PA5202 PA5202 hypothetical protein (NCBI) 253, 451
PA5209 PA5209 hypothetical protein (NCBI) 451, 452
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 PA0933
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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