Organism : Pseudomonas aeruginosa | Module List :
PA3515

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
cytoplasm go/ cellular_component
protein methylation go/ biological_process
protein methyltransferase activity go/ molecular_function
lipid biosynthetic process go/ biological_process
cyclopropane-fatty-acyl-phospholipid synthase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3515
(Mouseover regulator name to see its description)

PA3515 is regulated by 24 influences and regulates 0 modules.
Regulators for PA3515 (24)
Regulator Module Operator
PA0367 473 tf
PA0376 473 tf
PA1455 473 tf
PA1663 473 tf
PA1898 473 tf
PA2320 473 tf
PA3341 473 tf
PA3420 473 tf
PA3879 473 tf
PA4057 473 tf
PA4275 473 tf
PA4769 473 tf
PA5157 473 tf
PA5356 473 tf
PA1539 407 tf
PA2838 407 tf
PA3045 407 tf
PA3249 407 tf
PA4057 407 tf
PA4581 407 tf
PA4878 407 tf
PA5032 407 tf
PA5344 407 tf
PA5562 407 tf

Warning: PA3515 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
3638 1.40e-04 tTgacctTGaCacgatggcAAtc
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3639 2.60e+02 gGaattCtCcTCGaATGaGttCC
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3762 3.60e-08 A.aAtttTttcaatAcacTtt
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3763 5.40e-04 atCaacaagaA
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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 PA3515

PA3515 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Methylase involved in ubiquinone/menaquinone biosynthesis cog/ cog
cytoplasm go/ cellular_component
protein methylation go/ biological_process
protein methyltransferase activity go/ molecular_function
lipid biosynthetic process go/ biological_process
cyclopropane-fatty-acyl-phospholipid synthase activity go/ molecular_function
Module neighborhood information for PA3515

PA3515 has total of 50 gene neighbors in modules 407, 473
Gene neighbors (50)
Gene Common Name Description Module membership
PA0221 PA0221 probable aminotransferase (NCBI) 425, 473
PA0737 PA0737 hypothetical protein (NCBI) 27, 407
PA0738 PA0738 hypothetical protein (NCBI) 105, 407
PA0740 PA0740 probable beta-lactamase (NCBI) 323, 407
PA1168 PA1168 hypothetical protein (NCBI) 34, 473
PA1169 PA1169 probable lipoxygenase (NCBI) 104, 473
PA1892 PA1892 hypothetical protein (NCBI) 197, 473
PA1893 PA1893 hypothetical protein (NCBI) 197, 473
PA1894 PA1894 hypothetical protein (NCBI) 411, 473
PA1895 PA1895 hypothetical protein (NCBI) 411, 473
PA1896 PA1896 hypothetical protein (NCBI) 411, 473
PA1897 PA1897 hypothetical protein (NCBI) 411, 473
PA2064 pcoB copper resistance protein B precursor (NCBI) 197, 407
PA2065 pcoA copper resistance protein A precursor (NCBI) 197, 407
PA2680 PA2680 probable quinone oxidoreductase (NCBI) 190, 473
PA2807 PA2807 hypothetical protein (NCBI) 407, 428
PA2808 PA2808 hypothetical protein (NCBI) 407, 434
PA2809 PA2809 probable two-component response regulator (NCBI) 407, 434
PA2880 PA2880 hypothetical protein (NCBI) 201, 407
PA3039 PA3039 probable transporter (NCBI) 473, 475
PA3488 PA3488 hypothetical protein (NCBI) 293, 473
PA3515 PA3515 hypothetical protein (NCBI) 407, 473
PA3516 PA3516 probable lyase (NCBI) 105, 407
PA3517 PA3517 probable lyase (NCBI) 105, 407
PA3518 PA3518 hypothetical protein (NCBI) 105, 407
PA3519 PA3519 hypothetical protein (NCBI) 407, 473
PA3521 PA3521 probable outer membrane protein precursor (NCBI) 105, 407
PA3522 PA3522 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 105, 407
PA3523 PA3523 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 105, 407
PA3920 PA3920 probable metal transporting P-type ATPase (NCBI) 226, 407
PA4142 PA4142 probable secretion protein (NCBI) 112, 473
PA4143 PA4143 probable toxin transporter (NCBI) 112, 473
PA4144 PA4144 probable outer membrane protein precursor (NCBI) 112, 473
PA4513 PA4513 probable oxidoreductase (NCBI) 173, 473
PA4514 PA4514 probable outer membrane receptor for iron transport (NCBI) 98, 473
PA4515 PA4515 putative hydroxylase (NCBI) 98, 473
PA4516 PA4516 hypothetical protein (NCBI) 98, 473
PA4650 PA4650 hypothetical protein (NCBI) 392, 473
PA4652 PA4652 hypothetical protein (NCBI) 401, 473
PA4825 mgtA Mg(2+) transport ATPase, P-type 2 (NCBI) 330, 407
PA4869 PA4869 hypothetical protein (NCBI) 26, 473
PA4878 PA4878 probable transcriptional regulator (NCBI) 407, 550
PA5087 PA5087 hypothetical protein (NCBI) 231, 473
PA5089 PA5089 hypothetical protein (NCBI) 241, 473
PA5090 PA5090 hypothetical protein (NCBI) 439, 473
PA5157 PA5157 probable transcriptional regulator (NCBI) 212, 473
PA5158 PA5158 probable outer membrane protein precursor (NCBI) 53, 473
PA5159 PA5159 multidrug resistance protein (NCBI) 20, 473
PA5160 PA5160 drug efflux transporter (NCBI) 366, 473
PA5205 PA5205 hypothetical protein (NCBI) 246, 473
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 PA3515
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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