Organism : Pseudomonas aeruginosa | Module List :
PA3470

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
NTP pyrophosphohydrolases including oxidative damage repair enzymes cog/ cog
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3470
(Mouseover regulator name to see its description)

PA3470 is regulated by 27 influences and regulates 0 modules.
Regulators for PA3470 (27)
Regulator Module Operator
PA0167 4 tf
PA1504 4 tf
PA1776 4 tf
PA1945 4 tf
PA3285 4 tf
PA3965 4 tf
PA4238 4 tf
PA4451 4 tf
PA4462 4 tf
PA4600 4 tf
PA4755 4 tf
PA4853 4 tf
PA5337 4 tf
PA5344 4 tf
PA0906 9 tf
PA1015 9 tf
PA1607 9 tf
PA1653 9 tf
PA1859 9 tf
PA2028 9 tf
PA2054 9 tf
PA2577 9 tf
PA2713 9 tf
PA3689 9 tf
PA3699 9 tf
PA4462 9 tf
PA4784 9 tf

Warning: PA3470 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
2844 2.10e+00 AAgcgaTaCTtTGCgCcAaaa
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2845 1.50e+02 aTCG...cCtTg.CgGccaTC
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2854 4.00e+04 AaacctactTTTaTGCGtt
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2855 8.70e+01 A..cTttgctttgtA.GgaAtatt
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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 PA3470

PA3470 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
NTP pyrophosphohydrolases including oxidative damage repair enzymes cog/ cog
hydrolase activity go/ molecular_function
Module neighborhood information for PA3470

PA3470 has total of 49 gene neighbors in modules 4, 9
Gene neighbors (49)
Gene Common Name Description Module membership
PA0195 pntA putative NAD(P) transhydrogenase subunit alpha 1 (NCBI) 9, 342
PA0196 pntB pyridine nucleotide transhydrogenase, beta subunit (NCBI) 9, 342
PA0257 PA0257 hypothetical protein (NCBI) 9, 450
PA0258 PA0258 hypothetical protein (NCBI) 9, 450
PA0320 PA0320 hypothetical protein (NCBI) 9, 212
PA0422 PA0422 hypothetical protein (NCBI) 8, 9
PA0423 PA0423 hypothetical protein (NCBI) 9, 436
PA0542 PA0542 hypothetical protein (NCBI) 9, 261
PA0599 PA0599 hypothetical protein (NCBI) 9, 53
PA0782 putA proline dehydrogenase PutA (NCBI) 4, 315
PA1182 PA1182 probable transcriptional regulator (NCBI) 9, 20
PA1206 PA1206 hypothetical protein (NCBI) 4, 100
PA1263 PA1263 hypothetical protein (NCBI) 9, 72
PA1816 dnaQ DNA polymerase III subunit epsilon (NCBI) 4, 78
PA1859 PA1859 probable transcriptional regulator (NCBI) 9, 295
PA1863 modA molybdate-binding periplasmic protein precursor ModA (NCBI) 9, 263
PA1898 qscR quorum-sensing control repressor (NCBI) 9, 20
PA1934 PA1934 hypothetical protein (NCBI) 9, 320
PA1942 PA1942 hypothetical protein (NCBI) 9, 108
PA2029 PA2029 hypothetical protein (NCBI) 4, 20
PA2128 cupA1 fimbrial subunit CupA1 (NCBI) 9, 461
PA2541 PA2541 probable CDP-alcohol phosphatidyltransferase (NCBI) 9, 487
PA2579 kynA hypothetical protein (NCBI) 4, 281
PA2813 PA2813 probable glutathione S-transferase (NCBI) 9, 108
PA2943 PA2943 phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI) 8, 9
PA3030 mobA molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI) 9, 187
PA3055 PA3055 hypothetical protein (NCBI) 9, 452
PA3295 PA3295 probable HIT family protein (NCBI) 4, 368
PA3468 PA3468 hypothetical protein (NCBI) 4, 78
PA3469 PA3469 hypothetical protein (NCBI) 4, 9
PA3470 PA3470 hypothetical protein (NCBI) 4, 9
PA3538 PA3538 probable ATP-binding component of ABC transporter (NCBI) 4, 499
PA3575 PA3575 hypothetical protein (NCBI) 9, 224
PA3779 PA3779 hypothetical protein (NCBI) 9, 16
PA3965 PA3965 probable transcriptional regulator (NCBI) 4, 477
PA4114 PA4114 spermidine acetyltransferase (NCBI) 9, 245
PA4139 PA4139 hypothetical protein (NCBI) 9, 371
PA4454 PA4454 hypothetical protein (NCBI) 4, 341
PA4625 PA4625 hypothetical protein (NCBI) 9, 39
PA4784 PA4784 probable transcriptional regulator (NCBI) 9, 268
PA5122 PA5122 hypothetical protein (NCBI) 9, 477
PA5233 PA5233 flagellar protein (NCBI) 9, 368
PA5268 corA magnesium/cobalt transport protein (NCBI) 4, 368
PA5269 PA5269 hypothetical protein (NCBI) 4, 368
PA5270 PA5270 hypothetical protein (NCBI) 4, 368
PA5317 PA5317 probable binding protein component of ABC dipeptide transporter (NCBI) 4, 380
PA5362 PA5362 hypothetical protein (NCBI) 4, 398
PA5428 PA5428 probable transcriptional regulator (NCBI) 9, 283
PA5533 PA5533 hypothetical protein (NCBI) 9, 187
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 PA3470
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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