Organism : Pseudomonas aeruginosa | Module List :
PA0065

hypothetical protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted phosphatases cog/ cog
metabolic process go/ biological_process
phosphoglycolate phosphatase activity go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0065
(Mouseover regulator name to see its description)

PA0065 is regulated by 45 influences and regulates 0 modules.
Regulators for PA0065 (45)
Regulator Module Operator
PA0225 293 tf
PA0393 293 tf
PA0479 293 tf
PA0527 293 tf
PA0547 293 tf
PA0652 293 tf
PA0707 293 tf
PA0784 293 tf
PA0893 293 tf
PA1099 293 tf
PA1264 293 tf
PA1864 293 tf
PA2054 293 tf
PA2196 293 tf
PA2312 293 tf
PA2387 293 tf
PA2511 293 tf
PA2713 293 tf
PA2736 293 tf
PA2899 293 tf
PA3002 293 tf
PA3135 293 tf
PA3266 293 tf
PA3895 293 tf
PA3965 293 tf
PA4094 293 tf
PA4227 293 tf
PA4270 293 tf
PA4547 293 tf
PA0275 174 tf
PA0893 174 tf
PA1484 174 tf
PA1945 174 tf
PA2622 174 tf
PA3002 174 tf
PA3563 174 tf
PA3804 174 tf
PA4052 174 tf
PA4070 174 tf
PA4269 174 tf
PA4270 174 tf
PA4600 174 tf
PA5261 174 tf
PA5550 174 tf
PA5562 174 tf

Warning: PA0065 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
3176 6.40e+02 AtTTccTtAttcA
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3177 7.00e+02 gtGAaTCgctTtat
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3414 2.60e-05 AaaaCcagACcaTctTaAAtAcAA
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3415 4.00e+00 AcTtTTCc
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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 PA0065

PA0065 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted phosphatases cog/ cog
metabolic process go/ biological_process
phosphoglycolate phosphatase activity go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA0065

PA0065 has total of 35 gene neighbors in modules 174, 293
Gene neighbors (35)
Gene Common Name Description Module membership
PA0004 gyrB DNA gyrase subunit B (NCBI) 274, 293
PA0016 trkA potassium uptake protein TrkA (NCBI) 174, 274
PA0017 PA0017 hypothetical protein (NCBI) 174, 274
PA0018 fmt methionyl-tRNA formyltransferase (NCBI) 174, 274
PA0064 PA0064 hypothetical protein (NCBI) 293, 374
PA0065 PA0065 hypothetical protein (NCBI) 174, 293
PA0066 PA0066 hypothetical protein (NCBI) 165, 293
PA0067 prlC oligopeptidase A (NCBI) 293, 393
PA0068 PA0068 hypothetical protein (NCBI) 191, 293
PA0666 PA0666 hypothetical protein (NCBI) 174, 263
PA1086 flgK flagellar hook-associated protein (NCBI) 293, 347
PA1087 flgL flagellar hook-associated protein type 3 FlgL (NCBI) 293, 347
PA1088 PA1088 hypothetical protein (NCBI) 293, 347
PA1089 PA1089 hypothetical protein (NCBI) 293, 347
PA1090 PA1090 hypothetical protein (NCBI) 293, 347
PA1091 PA1091 hypothetical protein (NCBI) 293, 347
PA1494 PA1494 hypothetical protein (NCBI) 87, 293
PA1795 cysS cysteinyl-tRNA synthetase (NCBI) 174, 426
PA2739 pheT phenylalanyl-tRNA synthetase beta subunit (NCBI) 75, 174
PA3164 PA3164 still frameshift 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE prephenate dehydrogenase (NCBI) 174, 427
PA3165 hisC2 putative aminotransferase (NCBI) 174, 260
PA3171 ubiG 3-demethylubiquinone-9 3-methyltransferase (NCBI) 198, 293
PA3299 fadD1 long-chain-fatty-acid--CoA ligase (NCBI) 293, 389
PA3488 PA3488 hypothetical protein (NCBI) 293, 473
PA3632 PA3632 hypothetical protein (NCBI) 174, 270
PA4447 hisC1 histidinol-phosphate aminotransferase (NCBI) 174, 353
PA4601 morA motility regulator (NCBI) 60, 174
PA4687 hitA ferric iron-binding periplasmic protein HitA (NCBI) 98, 293
PA4688 hitB iron (III)-transport system permease HitB (NCBI) 49, 293
PA5003 PA5003 hypothetical protein (NCBI) 174, 270
PA5005 PA5005 probable carbamoyl transferase (NCBI) 174, 332
PA5161 rmlB dTDP-D-glucose 4,6-dehydratase (NCBI) 198, 293
PA5321 dut deoxyuridine 5'-triphosphate nucleotidohydrolase (NCBI) 174, 480
PA5413 ltaA low specificity l-threonine aldolase (NCBI) 293, 420
PA5493 polA DNA polymerase I (NCBI) 174, 263
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 PA0065
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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