Organism : Pseudomonas aeruginosa | Module List :
PA5388

hypothetical protein (NCBI)

CircVis
Functional Annotations (6)
Function System
ABC-type proline/glycine betaine transport systems, periplasmic components cog/ cog
transporter activity go/ molecular_function
binding go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
ABC_choline_bnd tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5388
(Mouseover regulator name to see its description)

PA5388 is regulated by 30 influences and regulates 0 modules.
Regulators for PA5388 (30)
Regulator Module Operator
PA0218 236 tf
PA0877 236 tf
PA1264 236 tf
PA1455 236 tf
PA1998 236 tf
PA2547 236 tf
PA2846 236 tf
PA3133 236 tf
PA3571 236 tf
PA3599 236 tf
PA3699 236 tf
PA3757 236 tf
PA4147 236 tf
PA4169 236 tf
PA5116 236 tf
PA5437 236 tf
PA0152 536 tf
PA0477 536 tf
PA1264 536 tf
PA1374 536 tf
PA2838 536 tf
PA3398 536 tf
PA3420 536 tf
PA3433 536 tf
PA3757 536 tf
PA4080 536 tf
PA4184 536 tf
PA4902 536 tf
PA5293 536 tf
PA5382 536 tf

Warning: PA5388 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
3300 2.90e-12 ACAACAAtaaattc
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3301 2.00e-03 aAgAaaATGAGTtT
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3884 1.80e-13 A.agAaActATc.gcttcA.t.AT
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3885 6.30e-05 aAaaa.aAgAACagg
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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 PA5388

PA5388 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type proline/glycine betaine transport systems, periplasmic components cog/ cog
transporter activity go/ molecular_function
binding go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
ABC_choline_bnd tigr/ tigrfam
Module neighborhood information for PA5388

PA5388 has total of 51 gene neighbors in modules 236, 536
Gene neighbors (51)
Gene Common Name Description Module membership
PA0152 pcaQ transcriptional regulator PcaQ (NCBI) 351, 536
PA0153 pcaH protocatechuate 3,4-dioxygenase, beta subunit (NCBI) 292, 536
PA0154 pcaG protocatechuate 3,4-dioxygenase, alpha subunit (NCBI) 196, 536
PA0218 PA0218 probable transcriptional regulator (NCBI) 236, 394
PA0239 PA0239 hypothetical protein (NCBI) 266, 536
PA0247 pobA 4-hydroxybenzoate 3-monooxygenase (NCBI) 471, 536
PA0477 PA0477 probable transcriptional regulator (NCBI) 536, 542
PA0529 PA0529 hypothetical protein (NCBI) 34, 536
PA0530 PA0530 probable class III pyridoxal phosphate-dependent aminotransferase (NCBI) 536, 550
PA0531 PA0531 probable glutamine amidotransferase (NCBI) 23, 536
PA1264 PA1264 probable transcriptional regulator (NCBI) 192, 536
PA1265 PA1265 hypothetical protein (NCBI) 333, 536
PA1499 PA1499 hypothetical protein (NCBI) 236, 372
PA1500 PA1500 probable oxidoreductase (NCBI) 236, 373
PA1501 PA1501 hypothetical protein (NCBI) 236, 373
PA1507 PA1507 probable transporter (NCBI) 24, 236
PA1514 PA1514 ureidoglycolate hydrolase (NCBI) 236, 328
PA1515 alc allantoicase (NCBI) 236, 328
PA1547 PA1547 hypothetical protein (NCBI) 53, 236
PA1577 PA1577 hypothetical protein (NCBI) 236, 344
PA1626 PA1626 probable major facilitator superfamily (MFS) transporter (NCBI) 236, 438
PA1920 PA1920 anaerobic ribonucleoside triphosphate reductase (NCBI) 236, 333
PA1927 metE 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (NCBI) 152, 236
PA1993 PA1993 hypothetical protein (NCBI) 196, 236
PA3398 PA3398 probable transcriptional regulator (NCBI) 536, 542
PA3433 PA3433 probable transcriptional regulator (NCBI) 61, 536
PA3560 fruA phosphotransferase system, fructose-specific IIBC component (NCBI) 236, 313
PA3561 fruK 1-phosphofructokinase (NCBI) 236, 536
PA3562 PA3562 probable phosphotransferase system enzyme I (NCBI) 236, 536
PA3564 PA3564 hypothetical protein (NCBI) 206, 236
PA3571 mmsR transcriptional regulator MmsR (NCBI) 236, 335
PA3598 PA3598 hypothetical protein (NCBI) 236, 334
PA3599 PA3599 probable transcriptional regulator (NCBI) 236, 334
PA4062 PA4062 hypothetical protein (NCBI) 23, 236
PA4081 cupB6 fimbrial subunit CupB6 (NCBI) 235, 536
PA4146 PA4146 hypothetical protein (NCBI) 175, 536
PA4147 acoR transcriptional regulator AcoR (NCBI) 236, 443
PA4169 PA4169 hypothetical protein (NCBI) 48, 236
PA4170 PA4170 hypothetical protein (NCBI) 236, 326
PA4184 PA4184 probable transcriptional regulator (NCBI) 61, 536
PA4622 PA4622 probable major facilitator superfamily (MFS) transporter (NCBI) 236, 377
PA4692 PA4692 hypothetical protein (NCBI) 157, 236
PA4849 PA4849 hypothetical protein (NCBI) 65, 236
PA4898 PA4898 probable porin (NCBI) 536, 538
PA4902 PA4902 probable transcriptional regulator (NCBI) 536, 538
PA4980 PA4980 probable enoyl-CoA hydratase/isomerase (NCBI) 125, 536
PA5287 amtB ammonium transporter AmtB (NCBI) 236, 245
PA5293 PA5293 probable transcriptional regulator (NCBI) 394, 536
PA5382 PA5382 probable transcriptional regulator (NCBI) 30, 536
PA5383 PA5383 hypothetical protein (NCBI) 30, 536
PA5388 PA5388 hypothetical protein (NCBI) 236, 536
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 PA5388
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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