Organism : Pseudomonas aeruginosa | Module List :
PA3313

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
ABC-type phosphate/phosphonate transport system, periplasmic component cog/ cog
phosphonate transmembrane transporter activity go/ molecular_function
phosphonate transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
3A0109s03R tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3313
(Mouseover regulator name to see its description)

PA3313 is regulated by 74 influences and regulates 0 modules.
Regulators for PA3313 (74)
Regulator Module Operator
PA0167 420 tf
PA0393 420 tf
PA0436 420 tf
PA0611 420 tf
PA0839 420 tf
PA0890 420 tf
PA1136 420 tf
PA1539 420 tf
PA1859 420 tf
PA1864 420 tf
PA2054 420 tf
PA2320 420 tf
PA2825 420 tf
PA2849 420 tf
PA2897 420 tf
PA3002 420 tf
PA3027 420 tf
PA3714 420 tf
PA3927 420 tf
PA4052 420 tf
PA4057 420 tf
PA4238 420 tf
PA4269 420 tf
PA4596 420 tf
PA4755 420 tf
PA5253 420 tf
PA5342 420 tf
PA5344 420 tf
PA0218 234 tf
PA0393 234 tf
PA0610 234 tf
PA0762 234 tf
PA0890 234 tf
PA0893 234 tf
PA1136 234 tf
PA1159 234 tf
PA1223 234 tf
PA1264 234 tf
PA1309 234 tf
PA1312 234 tf
PA1363 234 tf
PA1380 234 tf
PA1403 234 tf
PA1599 234 tf
PA1759 234 tf
PA1760 234 tf
PA1850 234 tf
PA1859 234 tf
PA1945 234 tf
PA2020 234 tf
PA2056 234 tf
PA2118 234 tf
PA2121 234 tf
PA2489 234 tf
PA2577 234 tf
PA2601 234 tf
PA2737 234 tf
PA2896 234 tf
PA3604 234 tf
PA3678 234 tf
PA3921 234 tf
PA3965 234 tf
PA4070 234 tf
PA4270 234 tf
PA4436 234 tf
PA4755 234 tf
PA4778 234 tf
PA4787 234 tf
PA5261 234 tf
PA5288 234 tf
PA5308 234 tf
PA5337 234 tf
PA5344 234 tf
PA5380 234 tf

Warning: PA3313 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
3296 7.90e-01 aAAcAAgA
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3297 2.70e+02 AcggttgcGCtgcCtTCcCtT
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3662 2.00e+03 AGGaAAAAcGc
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3663 1.90e+04 AgGAAatC
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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 PA3313

PA3313 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type phosphate/phosphonate transport system, periplasmic component cog/ cog
phosphonate transmembrane transporter activity go/ molecular_function
phosphonate transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
3A0109s03R tigr/ tigrfam
Module neighborhood information for PA3313

PA3313 has total of 47 gene neighbors in modules 234, 420
Gene neighbors (47)
Gene Common Name Description Module membership
PA0301 spuE polyamine transport protein (NCBI) 215, 234
PA0302 spuF polyamine transport protein PotG (NCBI) 215, 234
PA0303 spuG polyamine transport protein PotH (NCBI) 215, 234
PA0304 spuH polyamine transport protein PotI (NCBI) 215, 234
PA0353 ilvD dihydroxy-acid dehydratase (NCBI) 42, 420
PA0421 PA0421 hypothetical protein (NCBI) 78, 420
PA0550 PA0550 hypothetical protein (NCBI) 175, 420
PA0603 PA0603 probable ATP-binding component of ABC transporter (NCBI) 234, 338
PA0604 PA0604 probable binding protein component of ABC transporter (NCBI) 234, 338
PA0605 PA0605 probable permease of ABC transporter (NCBI) 20, 234
PA0606 PA0606 probable permease of ABC transporter (NCBI) 234, 337
PA0651 trpC indole-3-glycerol-phosphate synthase (NCBI) 8, 420
PA0934 relA GTP pyrophosphokinase (NCBI) 420, 462
PA0958 oprD Basic amino acid, basic peptide and imipenem outer membrane porin OprD precursor (NCBI) 193, 234
PA1047 PA1047 probable esterase (NCBI) 220, 420
PA1073 braD branched-chain amino acid transport protein BraD (NCBI) 193, 234
PA1171 PA1171 probable transglycolase (NCBI) 268, 420
PA1288 PA1288 probable outer membrane protein precursor (NCBI) 113, 234
PA1940 PA1940 hypothetical protein (NCBI) 234, 389
PA1941 PA1941 hypothetical protein (NCBI) 234, 389
PA2760 PA2760 probable outer membrane protein precursor (NCBI) 234, 237
PA3028 moeA2 molybdenum cofactor biosynthesis protein A2 (NCBI) 420, 540
PA3081 PA3081 hypothetical protein (NCBI) 120, 234
PA3082 gbt glycine betaine transmethylase (NCBI) 218, 234
PA3313 PA3313 hypothetical protein (NCBI) 234, 420
PA3314 PA3314 probable ATP-binding component of ABC transporter (NCBI) 420, 478
PA3357 dsdA D-serine dehydratase (NCBI) 420, 524
PA3481 PA3481 hypothetical protein (NCBI) 420, 540
PA3674 PA3674 hypothetical protein (NCBI) 238, 420
PA3836 PA3836 hypothetical protein (NCBI) 193, 234
PA3837 PA3837 probable permease of ABC transporter (NCBI) 193, 234
PA3838 PA3838 probable ATP-binding component of ABC transporter (NCBI) 193, 234
PA4605 PA4605 hypothetical protein (NCBI) 234, 511
PA4606 PA4606 hypothetical protein (NCBI) 193, 234
PA4655 hemH ferrochelatase (NCBI) 420, 477
PA4689 PA4689 hypothetical protein (NCBI) 420, 493
PA4715 PA4715 hypothetical protein (NCBI) 91, 420
PA4907 PA4907 probable short-chain dehydrogenase (NCBI) 42, 420
PA5075 PA5075 probable permease of ABC transporter (NCBI) 151, 234
PA5076 PA5076 probable binding protein component of ABC transporter (NCBI) 143, 234
PA5079 PA5079 D-tyrosyl-tRNA deacylase (NCBI) 420, 462
PA5146 PA5146 hypothetical protein (NCBI) 420, 435
PA5152 PA5152 probable ATP-binding component of ABC transporter (NCBI) 193, 234
PA5154 PA5154 probable permease of ABC transporter (NCBI) 193, 234
PA5155 PA5155 probable permease of ABC transporter (NCBI) 193, 234
PA5214 gcvH1 glycine cleavage system protein H1 (NCBI) 42, 420
PA5413 ltaA low specificity l-threonine aldolase (NCBI) 293, 420
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 PA3313
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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