Organism : Pseudomonas aeruginosa | Module List :
PA3785

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 PA3785
(Mouseover regulator name to see its description)

PA3785 is regulated by 25 influences and regulates 0 modules.
Regulators for PA3785 (25)
Regulator Module Operator
PA0179 46 tf
PA3604 46 tf
PA3622 46 tf
PA4132 46 tf
PA4493 46 tf
PA5437 46 tf
PA0125 462 tf
PA0167 462 tf
PA0393 462 tf
PA2047 462 tf
PA2076 462 tf
PA2519 462 tf
PA3126 462 tf
PA3689 462 tf
PA3714 462 tf
PA3778 462 tf
PA4080 462 tf
PA4269 462 tf
PA4493 462 tf
PA4596 462 tf
PA5059 462 tf
PA5253 462 tf
PA5261 462 tf
PA5342 462 tf
PA5437 462 tf

Warning: PA3785 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
2924 3.20e-04 AgaAacacgatcG.TgAggGctgT
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2925 3.00e+01 atCcTgTCGcCAtaaaCaGGcgcG
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3740 1.30e+03 cgacGG.aAAaaAccagtcat
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3741 1.10e+04 cgCaTcCtTcT
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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 PA3785

PA3785 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for PA3785

PA3785 has total of 42 gene neighbors in modules 46, 462
Gene neighbors (42)
Gene Common Name Description Module membership
PA0023 qor quinone oxidoreductase (NCBI) 7, 462
PA0050 PA0050 hypothetical protein (NCBI) 46, 291
PA0407 gshB glutathione synthetase (NCBI) 462, 488
PA0459 PA0459 probable ClpA/B protease ATP binding subunit (NCBI) 46, 413
PA0713 PA0713 hypothetical protein (NCBI) 46, 127
PA0934 relA GTP pyrophosphokinase (NCBI) 420, 462
PA1033 PA1033 probable glutathione S-transferase (NCBI) 462, 523
PA1123 PA1123 hypothetical protein (NCBI) 46, 127
PA1292 PA1292 probable 3-mercaptopyruvate sulfurtransferase (NCBI) 462, 523
PA1548 PA1548 hypothetical protein (NCBI) 46, 511
PA1549 PA1549 probable cation-transporting P-type ATPase (NCBI) 46, 511
PA1550 PA1550 hypothetical protein (NCBI) 46, 167
PA1551 PA1551 probable ferredoxin (NCBI) 46, 167
PA1654 PA1654 probable aminotransferase (NCBI) 151, 462
PA1655 PA1655 probable glutathione S-transferase (NCBI) 151, 462
PA2575 PA2575 hypothetical protein (NCBI) 436, 462
PA2788 PA2788 probable chemotaxis transducer (NCBI) 176, 462
PA2952 etfB electron transfer flavoprotein beta-subunit (NCBI) 342, 462
PA3043 PA3043 deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 7, 462
PA3118 leuB 3-isopropylmalate dehydrogenase (NCBI) 338, 462
PA3471 PA3471 probable malic enzyme (NCBI) 7, 462
PA3784 PA3784 hypothetical protein (NCBI) 46, 462
PA3785 PA3785 hypothetical protein (NCBI) 46, 462
PA3790 oprC Putative copper transport outer membrane porin OprC precursor (NCBI) 389, 462
PA3791 PA3791 hypothetical protein (NCBI) 46, 462
PA3928 PA3928 hypothetical protein (NCBI) 46, 64
PA3929 cioB cyanide insensitive terminal oxidase (NCBI) 46, 64
PA3930 cioA cyanide insensitive terminal oxidase (NCBI) 46, 64
PA4129 PA4129 hypothetical protein (NCBI) 46, 250
PA4130 PA4130 probable sulfite or nitrite reductase (NCBI) 46, 250
PA4131 PA4131 probable iron-sulfur protein (NCBI) 46, 250
PA4132 PA4132 hypothetical protein (NCBI) 46, 250
PA4133 PA4133 cytochrome c oxidase subunit (cbb3-type) (NCBI) 46, 250
PA4134 PA4134 hypothetical protein (NCBI) 46, 250
PA4308 PA4308 hypothetical protein (NCBI) 338, 462
PA4335 PA4335 hypothetical protein (NCBI) 443, 462
PA4841 PA4841 hypothetical protein (NCBI) 2, 462
PA5079 PA5079 D-tyrosyl-tRNA deacylase (NCBI) 420, 462
PA5080 PA5080 prolyl aminopeptidase (NCBI) 123, 462
PA5257 PA5257 hypothetical protein (NCBI) 316, 462
PA5496 PA5496 hypothetical protein (NCBI) 191, 462
PA5497 PA5497 hypothetical protein (NCBI) 191, 462
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 PA3785
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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