Organism : Pseudomonas aeruginosa | Module List :
PA1004 nadA

quinolinate synthetase (NCBI)

CircVis
Functional Annotations (6)
Function System
Quinolinate synthase cog/ cog
quinolinate synthetase A activity go/ molecular_function
NAD biosynthetic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
nadA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1004
(Mouseover regulator name to see its description)

PA1004 is regulated by 30 influences and regulates 0 modules.
Regulators for PA1004 nadA (30)
Regulator Module Operator
PA0376 251 tf
PA0424 251 tf
PA0762 251 tf
PA1520 251 tf
PA1853 251 tf
PA2123 251 tf
PA2692 251 tf
PA3034 251 tf
PA3266 251 tf
PA4451 251 tf
PA4745 251 tf
PA4764 251 tf
PA5337 251 tf
PA5438 251 tf
PA0376 165 tf
PA1201 165 tf
PA1269 165 tf
PA1422 165 tf
PA1520 165 tf
PA2076 165 tf
PA2467 165 tf
PA3927 165 tf
PA3932 165 tf
PA3965 165 tf
PA4057 165 tf
PA4755 165 tf
PA4769 165 tf
PA4853 165 tf
PA5301 165 tf
PA5344 165 tf

Warning: PA1004 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
3158 2.90e-07 ctTcgGCAggCgCGgG..GCCGCC
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3159 3.00e-06 gGCCctGctcGAaTaCagGCacAA
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3330 3.10e+02 AtACTgCaAAccgTC
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3331 3.10e+04 aAAAgcCcGatCctAcccgaa
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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 PA1004

PA1004 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Quinolinate synthase cog/ cog
quinolinate synthetase A activity go/ molecular_function
NAD biosynthetic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
nadA tigr/ tigrfam
Module neighborhood information for PA1004

PA1004 has total of 51 gene neighbors in modules 165, 251
Gene neighbors (51)
Gene Common Name Description Module membership
PA0042 PA0042 hypothetical protein (NCBI) 143, 165
PA0066 PA0066 hypothetical protein (NCBI) 165, 293
PA0461 PA0461 hypothetical protein (NCBI) 165, 368
PA0761 nadB L-aspartate oxidase (NCBI) 94, 165
PA0805 PA0805 hypothetical protein (NCBI) 251, 460
PA1004 nadA quinolinate synthetase (NCBI) 165, 251
PA1296 PA1296 probable 2-hydroxyacid dehydrogenase (NCBI) 251, 460
PA1440 PA1440 hypothetical protein (NCBI) 41, 251
PA1520 PA1520 probable transcriptional regulator (NCBI) 143, 165
PA1614 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (NCBI) 165, 198
PA1792 PA1792 UDP-2,3-diacylglucosamine hydrolase (NCBI) 165, 477
PA2117 PA2117 hypothetical protein (NCBI) 20, 165
PA2118 ada O6-methylguanine-DNA methyltransferase (NCBI) 165, 313
PA2979 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase (NCBI) 72, 165
PA2980 PA2980 hypothetical protein (NCBI) 143, 165
PA3004 PA3004 purine nucleoside phosphorylase (NCBI) 165, 220
PA3005 nagZ beta-hexosaminidase (NCBI) 72, 165
PA3046 PA3046 hypothetical protein (NCBI) 165, 541
PA3113 trpF N-(5'-phosphoribosyl)anthranilate isomerase (NCBI) 251, 309
PA3266 capB cold acclimation protein B (NCBI) 210, 251
PA3270 PA3270 hypothetical protein (NCBI) 251, 455
PA3286 PA3286 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 165, 256
PA3496 PA3496 hypothetical protein (NCBI) 165, 541
PA3664 PA3664 hypothetical protein (NCBI) 251, 412
PA3737 dsbC thiol:disulfide interchange protein DsbC (NCBI) 103, 251
PA4325 PA4325 hypothetical protein (NCBI) 251, 455
PA4360 PA4360 hypothetical protein (NCBI) 165, 224
PA4378 inaA InaA protein (NCBI) 251, 455
PA4379 PA4379 hypothetical protein (NCBI) 251, 455
PA4473 PA4473 hypothetical protein (NCBI) 165, 477
PA4572 fklB peptidyl-prolyl cis-trans isomerase FklB (NCBI) 232, 251
PA4764 fur ferric uptake regulation protein (NCBI) 251, 455
PA4765 omlA Outer membrane lipoprotein OmlA precursor (NCBI) 228, 251
PA4767 PA4767 hypothetical protein (NCBI) 139, 251
PA4850 prmA ribosomal protein L11 methyltransferase (NCBI) 122, 165
PA4963 PA4963 hypothetical protein (NCBI) 41, 251
PA5073 PA5073 hypothetical protein (NCBI) 187, 251
PA5143 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 165, 544
PA5176 PA5176 hypothetical protein (NCBI) 139, 251
PA5184 PA5184 chorismate mutase (NCBI) 178, 251
PA5195 PA5195 probable heat shock protein (NCBI) 165, 523
PA5196 PA5196 hypothetical protein (NCBI) 165, 477
PA5240 trxA thioredoxin (NCBI) 210, 251
PA5247 PA5247 hypothetical protein (NCBI) 251, 296
PA5285 PA5285 hypothetical protein (NCBI) 165, 541
PA5347 PA5347 hypothetical protein (NCBI) 143, 251
PA5363 PA5363 hypothetical protein (NCBI) 139, 251
PA5371 PA5371 hypothetical protein (NCBI) 243, 251
PA5438 PA5438 probable transcriptional regulator (NCBI) 251, 296
PA5490 cc4 cytochrome c4 precursor (NCBI) 165, 327
PA5515 PA5515 hypothetical protein (NCBI) 8, 251
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 PA1004
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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