Organism : Pseudomonas aeruginosa | Module List :
PA3085

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3085
(Mouseover regulator name to see its description)

PA3085 is regulated by 32 influences and regulates 0 modules.
Regulators for PA3085 (32)
Regulator Module Operator
PA1490 477 tf
PA1607 477 tf
PA2885 477 tf
PA2896 477 tf
PA3122 477 tf
PA3604 477 tf
PA3948 477 tf
PA3965 477 tf
PA4462 477 tf
PA4600 477 tf
PA4755 477 tf
PA4784 477 tf
PA4853 477 tf
PA5301 477 tf
PA5344 477 tf
PA5365 477 tf
PA5438 477 tf
PA0393 94 tf
PA0547 94 tf
PA1526 94 tf
PA1776 94 tf
PA3002 94 tf
PA3604 94 tf
PA3804 94 tf
PA3948 94 tf
PA4052 94 tf
PA4451 94 tf
PA4530 94 tf
PA4547 94 tf
PA4755 94 tf
PA5344 94 tf
PA5562 94 tf

Warning: PA3085 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
3020 1.60e+03 TTT.CcccT
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3021 1.60e+04 TTC.gAGTTT
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3770 7.80e-06 tAaaaatatGaAttagtGTgA
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3771 8.60e-04 cAtGgCTattgggaAtca..CTAT
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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 PA3085

PA3085 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for PA3085

PA3085 has total of 36 gene neighbors in modules 94, 477
Gene neighbors (36)
Gene Common Name Description Module membership
PA0398 PA0398 hypothetical protein (NCBI) 477, 541
PA0609 trpE anthranilate synthetase component I (NCBI) 8, 477
PA0650 trpD anthranilate phosphoribosyltransferase (NCBI) 8, 477
PA0761 nadB L-aspartate oxidase (NCBI) 94, 165
PA1031 PA1031 hypothetical protein (NCBI) 94, 384
PA1532 dnaX DNA polymerase III subunits gamma and tau (NCBI) 94, 178
PA1792 PA1792 UDP-2,3-diacylglucosamine hydrolase (NCBI) 165, 477
PA1842 PA1842 hypothetical protein (NCBI) 14, 94
PA1843 metH methionine synthase (NCBI) 14, 94
PA2613 PA2613 hypothetical protein (NCBI) 94, 390
PA2615 ftsK cell division protein FtsK (NCBI) 94, 296
PA2953 PA2953 electron transfer flavoprotein-ubiquinone oxidoreductase (NCBI) 342, 477
PA3070 PA3070 hypothetical protein (NCBI) 60, 94
PA3084 PA3084 hypothetical protein (NCBI) 94, 195
PA3085 PA3085 hypothetical protein (NCBI) 94, 477
PA3088 ppnK inorganic polyphosphate/ATP-NAD kinase (NCBI) 94, 477
PA3120 leuD isopropylmalate isomerase small subunit (NCBI) 381, 477
PA3121 leuC isopropylmalate isomerase large subunit (NCBI) 381, 477
PA3122 PA3122 probable transcriptional regulator (NCBI) 171, 477
PA3805 pilF type 4 fimbrial biogenesis protein PilF (NCBI) 94, 329
PA3948 PA3948 probable two-component response regulator (NCBI) 212, 477
PA3965 PA3965 probable transcriptional regulator (NCBI) 4, 477
PA4032 PA4032 probable two-component response regulator (NCBI) 477, 541
PA4033 PA4033 hypothetical protein (NCBI) 477, 541
PA4424 PA4424 hypothetical protein (NCBI) 94, 263
PA4473 PA4473 hypothetical protein (NCBI) 165, 477
PA4524 nadC nicotinate-nucleotide pyrophosphorylase (NCBI) 306, 477
PA4655 hemH ferrochelatase (NCBI) 420, 477
PA4676 PA4676 probable carbonic anhydrase (NCBI) 123, 477
PA4695 ilvH acetolactate synthase III small subunit (NCBI) 94, 543
PA4755 greA transcription elongation factor GreA (NCBI) 436, 477
PA5122 PA5122 hypothetical protein (NCBI) 9, 477
PA5134 PA5134 probable carboxyl-terminal protease (NCBI) 94, 499
PA5196 PA5196 hypothetical protein (NCBI) 165, 477
PA5360 phoB two-component response regulator PhoB (NCBI) 371, 477
PA5361 phoR two-component sensor PhoR (NCBI) 371, 477
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 PA3085
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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