Organism : Pseudomonas aeruginosa | Module List :
PA3129

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3129
(Mouseover regulator name to see its description)

PA3129 is regulated by 33 influences and regulates 0 modules.
Regulators for PA3129 (33)
Regulator Module Operator
PA0163 438 tf
PA0448 438 tf
PA1128 438 tf
PA1309 438 tf
PA1315 438 tf
PA1374 438 tf
PA1627 438 tf
PA1853 438 tf
PA2047 438 tf
PA3067 438 tf
PA3133 438 tf
PA5342 438 tf
PA0125 135 tf
PA0236 135 tf
PA1241 135 tf
PA1853 135 tf
PA2047 135 tf
PA2115 135 tf
PA2281 135 tf
PA2316 135 tf
PA2692 135 tf
PA2957 135 tf
PA3604 135 tf
PA3622 135 tf
PA3921 135 tf
PA4275 135 tf
PA4279 135 tf
PA4769 135 tf
PA4853 135 tf
PA4890 135 tf
PA5253 135 tf
PA5437 135 tf
PA5550 135 tf

Warning: PA3129 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
3100 1.50e-03 ccgtAcaaT..cCggCctTtt
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3101 1.30e+02 GAaGGtTccggaCa
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3696 1.90e-04 T.AGaa.acgTagCtAT.aTcATg
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3697 2.40e-03 cTgGCc.aGGAAgAA
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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 PA3129

PA3129 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
tRNA-dihydrouridine synthase cog/ cog
tRNA processing go/ biological_process
oxidoreductase activity go/ molecular_function
flavin adenine dinucleotide binding go/ molecular_function
Module neighborhood information for PA3129

PA3129 has total of 49 gene neighbors in modules 135, 438
Gene neighbors (49)
Gene Common Name Description Module membership
PA0128 PA0128 hypothetical protein (NCBI) 126, 135
PA0163 PA0163 probable transcriptional regulator (NCBI) 344, 438
PA0378 mtgA monofunctional biosynthetic peptidoglycan transglycosylase (NCBI) 181, 438
PA0379 PA0379 hypothetical protein (NCBI) 387, 438
PA0448 PA0448 probable transcriptional regulator (NCBI) 175, 438
PA0583 PA0583 hypothetical protein (NCBI) 135, 230
PA0736 PA0736 hypothetical protein (NCBI) 372, 438
PA0760 PA0760 hypothetical protein (NCBI) 135, 490
PA0775 PA0775 hypothetical protein (NCBI) 114, 135
PA0947 PA0947 hypothetical protein (NCBI) 135, 255
PA0975 PA0975 probable radical activating enzyme (NCBI) 135, 377
PA0976 PA0976 hypothetical protein (NCBI) 135, 143
PA1128 PA1128 probable transcriptional regulator (NCBI) 175, 438
PA1227 PA1227 hypothetical protein (NCBI) 101, 438
PA1291 PA1291 hypothetical protein (NCBI) 173, 438
PA1309 PA1309 probable transcriptional regulator (NCBI) 266, 438
PA1315 PA1315 probable transcriptional regulator (NCBI) 220, 438
PA1316 PA1316 probable major facilitator superfamily (MFS) transporter (NCBI) 408, 438
PA1373 fabF2 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 68, 438
PA1374 PA1374 hypothetical protein (NCBI) 68, 438
PA1425 PA1425 probable ATP-binding component of ABC transporter (NCBI) 335, 438
PA1563 PA1563 hypothetical protein (NCBI) 135, 374
PA1626 PA1626 probable major facilitator superfamily (MFS) transporter (NCBI) 236, 438
PA1627 PA1627 probable transcriptional regulator (NCBI) 306, 438
PA1652 PA1652 hypothetical protein (NCBI) 68, 438
PA1675 PA1675 hypothetical protein (NCBI) 135, 255
PA1790 PA1790 hypothetical protein (NCBI) 135, 344
PA1960 PA1960 hypothetical protein (NCBI) 245, 438
PA2281 PA2281 probable transcriptional regulator (NCBI) 135, 494
PA2315 PA2315 hypothetical protein (NCBI) 135, 344
PA2316 PA2316 probable transcriptional regulator (NCBI) 135, 344
PA2449 PA2449 probable transcriptional regulator (NCBI) 1, 135
PA2502 PA2502 hypothetical protein (NCBI) 135, 351
PA2563 PA2563 probable sulfate transporter (NCBI) 438, 507
PA3065 PA3065 hypothetical protein (NCBI) 324, 438
PA3066 PA3066 hypothetical protein (NCBI) 324, 438
PA3067 PA3067 probable transcriptional regulator (NCBI) 324, 438
PA3129 PA3129 hypothetical protein (NCBI) 135, 438
PA3312 PA3312 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 196, 438
PA3679 PA3679 hypothetical protein (NCBI) 335, 438
PA3680 PA3680 hypothetical protein (NCBI) 114, 438
PA3685 PA3685 hypothetical protein (NCBI) 111, 135
PA4390 PA4390 hypothetical protein (NCBI) 111, 135
PA4574 PA4574 hypothetical protein (NCBI) 111, 135
PA4609 radA DNA repair protein RadA (NCBI) 306, 438
PA4873 PA4873 probable heat-shock protein (NCBI) 135, 230
PA5048 PA5048 probable nuclease (NCBI) 135, 501
PA5412 PA5412 hypothetical protein (NCBI) 359, 438
PA5442 PA5442 hypothetical protein (NCBI) 266, 438
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 PA3129
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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