Organism : Pseudomonas aeruginosa | Module List :
PA1859

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 PA1859
(Mouseover regulator name to see its description)

PA1859 is regulated by 28 influences and regulates 20 modules.
Regulators for PA1859 (28)
Regulator Module Operator
PA0207 295 tf
PA0306 295 tf
PA1351 295 tf
PA1399 295 tf
PA1467 295 tf
PA1484 295 tf
PA1850 295 tf
PA2047 295 tf
PA2432 295 tf
PA2681 295 tf
PA2834 295 tf
PA3007 295 tf
PA3995 295 tf
PA4196 295 tf
PA4238 295 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: PA1859 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
2854 4.00e+04 AaacctactTTTaTGCGtt
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2855 8.70e+01 A..cTttgctttgtA.GgaAtatt
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3418 1.10e+00 tCgGtgc.tgCcGAagAaagC
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3419 2.30e+01 CcGATGAtcgATcCG
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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 PA1859

PA1859 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 PA1859

PA1859 has total of 69 gene neighbors in modules 9, 295
Gene neighbors (69)
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
PA0254 PA0254 hypothetical protein (NCBI) 295, 323
PA0257 PA0257 hypothetical protein (NCBI) 9, 450
PA0258 PA0258 hypothetical protein (NCBI) 9, 450
PA0306 PA0306 probable transcriptional regulator (NCBI) 295, 375
PA0320 PA0320 hypothetical protein (NCBI) 9, 212
PA0422 PA0422 hypothetical protein (NCBI) 8, 9
PA0423 PA0423 hypothetical protein (NCBI) 9, 436
PA0481 PA0481 hypothetical protein (NCBI) 291, 295
PA0542 PA0542 hypothetical protein (NCBI) 9, 261
PA0571 PA0571 hypothetical protein (NCBI) 62, 295
PA0599 PA0599 hypothetical protein (NCBI) 9, 53
PA1182 PA1182 probable transcriptional regulator (NCBI) 9, 20
PA1252 PA1252 probable L-malate dehydrogenase (NCBI) 180, 295
PA1263 PA1263 hypothetical protein (NCBI) 9, 72
PA1311 phnX 2-phosphonoacetaldehyde hydrolase (NCBI) 295, 486
PA1401 PA1401 hypothetical protein (NCBI) 295, 507
PA1415 PA1415 hypothetical protein (NCBI) 87, 295
PA1484 PA1484 probable transcriptional regulator (NCBI) 294, 295
PA1487 PA1487 probable carbohydrate kinase (NCBI) 295, 320
PA1488 PA1488 hypothetical protein (NCBI) 295, 375
PA1489 PA1489 hypothetical protein (NCBI) 295, 375
PA1495 PA1495 hypothetical protein (NCBI) 87, 295
PA1496 PA1496 probable potassium channel (NCBI) 20, 295
PA1648 PA1648 probable oxidoreductase (NCBI) 84, 295
PA1858 str streptomycin 3''-phosphotransferase (NCBI) 246, 295
PA1859 PA1859 probable transcriptional regulator (NCBI) 9, 295
PA1863 modA molybdate-binding periplasmic protein precursor ModA (NCBI) 9, 263
PA1878 PA1878 hypothetical protein (NCBI) 283, 295
PA1898 qscR quorum-sensing control repressor (NCBI) 9, 20
PA1929 PA1929 hypothetical protein (NCBI) 189, 295
PA1931 PA1931 probable ferredoxin (NCBI) 280, 295
PA1934 PA1934 hypothetical protein (NCBI) 9, 320
PA1936 PA1936 hypothetical protein (NCBI) 295, 445
PA1942 PA1942 hypothetical protein (NCBI) 9, 108
PA2095 PA2095 hypothetical protein (NCBI) 287, 295
PA2128 cupA1 fimbrial subunit CupA1 (NCBI) 9, 461
PA2541 PA2541 probable CDP-alcohol phosphatidyltransferase (NCBI) 9, 487
PA2813 PA2813 probable glutathione S-transferase (NCBI) 9, 108
PA2822 PA2822 hypothetical protein (NCBI) 295, 320
PA2824 PA2824 probable sensor/response regulator hybrid (NCBI) 206, 295
PA2833 PA2833 hypothetical protein (NCBI) 295, 486
PA2834 PA2834 probable transcriptional regulator (NCBI) 295, 486
PA2836 PA2836 probable secretion protein (NCBI) 295, 486
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
PA3076 PA3076 hypothetical protein (NCBI) 49, 295
PA3207 PA3207 hypothetical protein (NCBI) 295, 366
PA3318 PA3318 hypothetical protein (NCBI) 295, 366
PA3373 PA3373 hypothetical protein (NCBI) 109, 295
PA3469 PA3469 hypothetical protein (NCBI) 4, 9
PA3470 PA3470 hypothetical protein (NCBI) 4, 9
PA3575 PA3575 hypothetical protein (NCBI) 9, 224
PA3759 PA3759 probable aminotransferase (NCBI) 295, 523
PA3779 PA3779 hypothetical protein (NCBI) 9, 16
PA3995 PA3995 probable transcriptional regulator (NCBI) 295, 546
PA4114 PA4114 spermidine acetyltransferase (NCBI) 9, 245
PA4139 PA4139 hypothetical protein (NCBI) 9, 371
PA4380 PA4380 probable two-component sensor (NCBI) 53, 295
PA4625 PA4625 hypothetical protein (NCBI) 9, 39
PA4725 cbrA two-component sensor CbrA (NCBI) 268, 295
PA4784 PA4784 probable transcriptional regulator (NCBI) 9, 268
PA5122 PA5122 hypothetical protein (NCBI) 9, 477
PA5233 PA5233 flagellar protein (NCBI) 9, 368
PA5310 PA5310 hypothetical protein (NCBI) 295, 461
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 PA1859
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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