Organism : Pseudomonas aeruginosa | Module List :
PA3975 thiD

phosphomethylpyrimidine kinase (NCBI)

CircVis
Functional Annotations (4)
Function System
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase cog/ cog
phosphomethylpyrimidine kinase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3975
(Mouseover regulator name to see its description)

PA3975 is regulated by 35 influences and regulates 0 modules.
Regulators for PA3975 thiD (35)
Regulator Module Operator
PA3604 286 tf
PA3804 286 tf
PA3948 286 tf
PA4057 286 tf
PA4238 286 tf
PA4275 286 tf
PA4451 286 tf
PA4745 286 tf
PA4853 286 tf
PA5337 286 tf
PA5344 286 tf
PA0125 86 tf
PA0611 86 tf
PA1526 86 tf
PA1544 86 tf
PA1850 86 tf
PA2577 86 tf
PA2622 86 tf
PA3002 86 tf
PA3563 86 tf
PA3604 86 tf
PA3757 86 tf
PA4052 86 tf
PA4057 86 tf
PA4070 86 tf
PA4094 86 tf
PA4145 86 tf
PA4451 86 tf
PA4530 86 tf
PA4600 86 tf
PA4853 86 tf
PA5337 86 tf
PA5344 86 tf
PA5438 86 tf
PA5550 86 tf

Warning: PA3975 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
3004 1.60e+02 TAtaATgC
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3005 2.60e+02 TATccCaTTTcGcTtTCcCtCG
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3400 1.80e+00 TATaGTcCtgatAat
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3401 1.30e-01 CtCGGtGcCGGaGAGcCGGCGA
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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 PA3975

PA3975 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase cog/ cog
phosphomethylpyrimidine kinase activity go/ molecular_function
Thiamine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA3975

PA3975 has total of 34 gene neighbors in modules 86, 286
Gene neighbors (34)
Gene Common Name Description Module membership
PA0011 PA0011 lipid A biosynthesis lauroyl acyltransferase (NCBI) 62, 86
PA0335 PA0335 hypothetical protein (NCBI) 86, 398
PA0404 PA0404 Holliday junction resolvase-like protein (NCBI) 86, 278
PA0405 PA0405 hypothetical protein (NCBI) 86, 263
PA0406 PA0406 hypothetical protein (NCBI) 86, 332
PA0936 lpxO2 lipopolysaccharide biosynthetic protein LpxO2 (NCBI) 86, 212
PA0937 PA0937 hypothetical protein (NCBI) 281, 286
PA1543 apt adenine phosphoribosyltransferase (NCBI) 86, 214
PA1757 thrH homoserine kinase (NCBI) 249, 286
PA1857 PA1857 hypothetical protein (NCBI) 86, 398
PA1913 PA1913 hypothetical protein (NCBI) 86, 170
PA2817 PA2817 hypothetical protein (NCBI) 86, 195
PA2866 mttC secretion protein MttC (NCBI) 86, 103
PA3170 PA3170 N-ethylammeline chlorohydrolase (NCBI) 86, 130
PA3456 PA3456 hypothetical protein (NCBI) 86, 442
PA3686 adk adenylate kinase (NCBI) 123, 286
PA3968 PA3968 probable pseudouridine synthase (NCBI) 86, 229
PA3975 thiD phosphomethylpyrimidine kinase (NCBI) 86, 286
PA3976 thiE thiamine-phosphate diphosphorylase (NCBI) 106, 286
PA3987 leuS leucyl-tRNA synthetase (NCBI) 286, 398
PA4684 PA4684 hypothetical protein (NCBI) 86, 520
PA4722 PA4722 hypothetical protein (NCBI) 286, 384
PA4723 dksA suppressor protein DksA (NCBI) 122, 286
PA4724 PA4724 glutamyl-tRNA synthetase (NCBI) 286, 501
PA4948 PA4948 hypothetical protein (NCBI) 86, 306
PA4949 PA4949 hypothetical protein (NCBI) 86, 306
PA4950 PA4950 hypothetical protein (NCBI) 86, 306
PA4953 motB flagellar motor protein (NCBI) 8, 286
PA4954 motA flagellar motor protein (NCBI) 8, 286
PA4956 rhdA thiosulfate sulfurtransferase (NCBI) 286, 433
PA4957 psd phosphatidylserine decarboxylase (NCBI) 286, 433
PA5289 PA5289 hypothetical protein (NCBI) 86, 398
PA5414 PA5414 hypothetical protein (NCBI) 281, 286
PA5462 PA5462 hypothetical protein (NCBI) 276, 286
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 PA3975
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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