Organism : Pseudomonas aeruginosa | Module List :
PA1504

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1504
(Mouseover regulator name to see its description)

PA1504 is regulated by 33 influences and regulates 46 modules.
Regulators for PA1504 (33)
Regulator Module Operator
PA0167 78 tf
PA0279 78 tf
PA0961 78 tf
PA1490 78 tf
PA1504 78 tf
PA1945 78 tf
PA2896 78 tf
PA3285 78 tf
PA3458 78 tf
PA3604 78 tf
PA3804 78 tf
PA3845 78 tf
PA4238 78 tf
PA4547 78 tf
PA4755 78 tf
PA4853 78 tf
PA5344 78 tf
PA5550 78 tf
PA5562 78 tf
PA0763 62 tf
PA0791 62 tf
PA0893 62 tf
PA1125 62 tf
PA1526 62 tf
PA1653 62 tf
PA2028 62 tf
PA2115 62 tf
PA2267 62 tf
PA2736 62 tf
PA3002 62 tf
PA3583 62 tf
PA3778 62 tf
PA4703 62 tf

Warning: PA1504 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
2956 1.20e+01 tttcagTTTctC..cgaAAaaTT
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2957 3.00e+02 CgacaATTGaTC
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2988 6.00e+01 GgatCgattGgcAAAaaagaagtA
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2989 1.50e+02 aACGgCtcTGGcGtAtGCt
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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 PA1504

PA1504 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA1504

PA1504 has total of 55 gene neighbors in modules 62, 78
Gene neighbors (55)
Gene Common Name Description Module membership
PA0011 PA0011 lipid A biosynthesis lauroyl acyltransferase (NCBI) 62, 86
PA0041 PA0041 probable hemagglutinin (NCBI) 62, 337
PA0048 PA0048 probable transcriptional regulator (NCBI) 62, 187
PA0292 aguA agmatine deiminase (NCBI) 62, 263
PA0341 lgt prolipoprotein diacylglyceryl transferase (NCBI) 78, 493
PA0420 bioA adenosylmethionine--8-amino-7-oxononanoate transaminase (NCBI) 78, 433
PA0421 PA0421 hypothetical protein (NCBI) 78, 420
PA0504 bioD dithiobiotin synthetase (NCBI) 62, 253
PA0571 PA0571 hypothetical protein (NCBI) 62, 295
PA0659 PA0659 hypothetical protein (NCBI) 62, 76
PA0758 PA0758 hypothetical protein (NCBI) 78, 195
PA1032 PA1032 probable penicillin amidase (NCBI) 78, 396
PA1068 PA1068 probable heat shock protein (hsp90 family) (NCBI) 62, 487
PA1149 PA1149 hypothetical protein (NCBI) 62, 355
PA1207 kefB glutathione-regulated potassium-efflux system protein KefB (NCBI) 78, 100
PA1222 PA1222 probable membrane-bound lytic murein transglycolase A (NCBI) 62, 229
PA1504 PA1504 probable transcriptional regulator (NCBI) 62, 78
PA1526 PA1526 probable transcriptional regulator (NCBI) 62, 522
PA1688 PA1688 hypothetical protein (NCBI) 78, 329
PA1689 PA1689 hypothetical protein (NCBI) 78, 329
PA1726 bglX periplasmic beta-glucosidase (NCBI) 49, 62
PA1816 dnaQ DNA polymerase III subunit epsilon (NCBI) 4, 78
PA2267 PA2267 probable transcriptional regulator (NCBI) 62, 519
PA2289 PA2289 hypothetical protein (NCBI) 39, 62
PA2382 lldA L-lactate dehydrogenase (NCBI) 62, 290
PA2455 PA2455 hypothetical protein (NCBI) 62, 363
PA2457 PA2457 hypothetical protein (NCBI) 62, 206
PA2462 PA2462 hypothetical protein (NCBI) 62, 297
PA2962 tmk thymidylate kinase (NCBI) 1, 62
PA3020 PA3020 probable soluble lytic transglycosylase (NCBI) 62, 522
PA3086 PA3086 hypothetical protein (NCBI) 62, 387
PA3310 PA3310 hypothetical protein (NCBI) 78, 315
PA3468 PA3468 hypothetical protein (NCBI) 4, 78
PA3627 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI) 62, 139
PA3777 xseA exodeoxyribonuclease VII large subunit (NCBI) 62, 528
PA3778 PA3778 probable transcriptional regulator (NCBI) 62, 528
PA4056 ribD riboflavin-specific deaminase/reductase (NCBI) 62, 228
PA4331 PA4331 hypothetical protein (NCBI) 62, 443
PA4332 PA4332 hypothetical protein (NCBI) 62, 443
PA4356 xenB xenobiotic reductase (NCBI) 62, 108
PA4393 PA4393 probable permease (NCBI) 20, 62
PA4488 PA4488 hypothetical protein (NCBI) 62, 66
PA4517 PA4517 hypothetical protein (NCBI) 78, 206
PA4519 speC ornithine decarboxylase (NCBI) 78, 195
PA4546 pilS two-component sensor PilS (NCBI) 78, 480
PA4693 pssA phosphatidylserine synthase (NCBI) 78, 341
PA4721 PA4721 sugar fermentation stimulation protein (NCBI) 53, 62
PA4807 selB selenocysteine-specific elongation factor (NCBI) 49, 62
PA4839 speA arginine decarboxylase (NCBI) 78, 341
PA5014 glnE glutamate-ammonia-ligase adenylyltransferase (NCBI) 3, 62
PA5035 gltD glutamate synthase small chain (NCBI) 62, 189
PA5036 gltB glutamate synthase large chain precursor (NCBI) 62, 451
PA5038 aroB 3-dehydroquinate synthase (NCBI) 78, 528
PA5082 PA5082 probable binding protein component of ABC transporter (NCBI) 62, 74
PA5280 sss site-specific recombinase Sss (NCBI) 49, 62
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 PA1504
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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