Organism : Pseudomonas aeruginosa | Module List :
PA3711

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3711
(Mouseover regulator name to see its description)

PA3711 is regulated by 30 influences and regulates 40 modules.
Regulators for PA3711 (30)
Regulator Module Operator
PA0233 313 tf
PA0272 313 tf
PA0564 313 tf
PA0780 313 tf
PA2766 313 tf
PA3027 313 tf
PA3423 313 tf
PA3433 313 tf
PA3711 313 tf
PA4269 313 tf
PA4581 313 tf
PA4906 313 tf
PA5032 313 tf
PA5179 313 tf
PA1138 192 tf
PA1261 192 tf
PA1312 192 tf
PA1380 192 tf
PA2032 192 tf
PA3420 192 tf
PA3630 192 tf
PA3711 192 tf
PA3830 192 tf
PA4288 192 tf
PA4363 192 tf
PA5032 192 tf
PA5218 192 tf
PA5293 192 tf
PA5431 192 tf
PA5525 192 tf

Warning: PA3711 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
3212 1.40e-03 AtAcgTcTgTattcatattg
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3213 3.90e-01 TAtGaAAAAgGAAT
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3452 7.70e+02 GaaagGCcggCgAg
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3453 1.20e+04 ATCct.CGcTtcacc
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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 PA3711

PA3711 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA3711

PA3711 has total of 66 gene neighbors in modules 192, 313
Gene neighbors (66)
Gene Common Name Description Module membership
PA0142 PA0142 hydroxydechloroatrazine ethylaminohydrolase (NCBI) 175, 192
PA0182 PA0182 probable short-chain dehydrogenase (NCBI) 196, 313
PA0233 PA0233 probable transcriptional regulator (NCBI) 20, 313
PA0328 PA0328 hypothetical protein (NCBI) 313, 550
PA0347 glpQ glycerophosphoryl diester phosphodiesterase, periplasmic (NCBI) 105, 192
PA0544 PA0544 hypothetical protein (NCBI) 313, 375
PA0562 PA0562 probable hydrolase (NCBI) 58, 313
PA0676 PA0676 probable transmembrane sensor (NCBI) 192, 500
PA1138 PA1138 probable transcriptional regulator (NCBI) 192, 373
PA1143 PA1143 hypothetical protein (NCBI) 313, 425
PA1195 PA1195 hypothetical protein (NCBI) 68, 313
PA1264 PA1264 probable transcriptional regulator (NCBI) 192, 536
PA1282 PA1282 probable major facilitator superfamily (MFS) transporter (NCBI) 92, 192
PA1312 PA1312 probable transcriptional regulator (NCBI) 192, 537
PA1345 PA1345 hypothetical protein (NCBI) 192, 206
PA1503 PA1503 hypothetical protein (NCBI) 192, 425
PA1536 PA1536 hypothetical protein (NCBI) 313, 550
PA1595 PA1595 hypothetical protein (NCBI) 313, 335
PA1628 PA1628 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 61, 192
PA1635 kdpC potassium-transporting ATPase subunit C (NCBI) 192, 267
PA1636 kdpD two-component sensor KdpD (NCBI) 241, 313
PA1637 kdpE two-component response regulator KdpE (NCBI) 241, 313
PA1957 PA1957 hypothetical protein (NCBI) 313, 469
PA2032 PA2032 probable transcriptional regulator (NCBI) 192, 245
PA2118 ada O6-methylguanine-DNA methyltransferase (NCBI) 165, 313
PA2542 PA2542 hypothetical protein (NCBI) 157, 313
PA2543 PA2543 hypothetical protein (NCBI) 157, 313
PA2574 alkB1 alkane-1-monooxygenase (NCBI) 30, 192
PA2844 PA2844 hypothetical protein (NCBI) 283, 313
PA2949 PA2949 probable lipase (NCBI) 313, 432
PA3015 PA3015 hypothetical protein (NCBI) 245, 313
PA3092 fadH1 2,4-dienoyl-CoA reductase FadH1 (NCBI) 157, 313
PA3130 PA3130 hypothetical protein (NCBI) 229, 313
PA3206 PA3206 probable two-component sensor (NCBI) 175, 313
PA3288 PA3288 hypothetical protein (NCBI) 229, 313
PA3387 rhlG beta-ketoacyl reductase (NCBI) 192, 550
PA3423 PA3423 probable transcriptional regulator (NCBI) 313, 374
PA3464 PA3464 hypothetical protein (NCBI) 175, 192
PA3560 fruA phosphotransferase system, fructose-specific IIBC component (NCBI) 236, 313
PA3671 PA3671 probable permease of ABC transporter (NCBI) 104, 313
PA3711 PA3711 probable transcriptional regulator (NCBI) 192, 313
PA3718 PA3718 probable major facilitator superfamily (MFS) transporter (NCBI) 192, 309
PA3733 PA3733 hypothetical protein (NCBI) 175, 192
PA3867 PA3867 probable DNA invertase (NCBI) 173, 313
PA4036 PA4036 probable two-component sensor (NCBI) 20, 313
PA4038 PA4038 hypothetical protein (NCBI) 192, 267
PA4082 cupB5 adhesive protein CupB5 (NCBI) 175, 192
PA4092 hpaC 4-hydroxyphenylacetate 3-monooxygenase small chain (NCBI) 192, 337
PA4287 PA4287 hypothetical protein (NCBI) 177, 192
PA4288 PA4288 probable transcriptional regulator (NCBI) 192, 373
PA4330 PA4330 probable enoyl-CoA hydratase/isomerase (NCBI) 192, 443
PA4351 PA4351 probable acyltransferase (NCBI) 23, 192
PA4363 iciA chromosome replication initiation inhibitor protein (NCBI) 192, 372
PA4374 PA4374 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 245, 313
PA4539 PA4539 hypothetical protein (NCBI) 189, 313
PA4586 PA4586 hypothetical protein (NCBI) 192, 497
PA4592 PA4592 probable outer membrane protein precursor (NCBI) 313, 489
PA4593 PA4593 probable permease of ABC transporter (NCBI) 20, 313
PA4613 katB catalase (NCBI) 152, 313
PA4734 PA4734 hypothetical protein (NCBI) 313, 338
PA4779 PA4779 hypothetical protein (NCBI) 313, 337
PA5145 PA5145 hypothetical protein (NCBI) 245, 313
PA5179 PA5179 probable transcriptional regulator (NCBI) 253, 313
PA5218 PA5218 probable transcriptional regulator (NCBI) 20, 192
PA5381 PA5381 hypothetical protein (NCBI) 192, 345
PA5467 PA5467 hypothetical protein (NCBI) 70, 313
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 PA3711
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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