Organism : Pseudomonas aeruginosa | Module List :
PA0487

probable molybdenum transport regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
N-terminal domain of molybdenum-binding protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdate ion transport go/ biological_process
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
ModE_repress tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0487
(Mouseover regulator name to see its description)

PA0487 is regulated by 22 influences and regulates 6 modules.
Regulators for PA0487 (22)
Regulator Module Operator
PA0120 523 tf
PA0167 523 tf
PA0393 523 tf
PA0475 523 tf
PA0479 523 tf
PA0784 523 tf
PA0815 523 tf
PA0961 523 tf
PA1760 523 tf
PA2047 523 tf
PA2376 523 tf
PA2484 523 tf
PA2713 523 tf
PA2737 523 tf
PA2766 523 tf
PA3714 523 tf
PA3757 523 tf
PA3895 523 tf
PA4145 523 tf
PA4451 523 tf
PA5253 523 tf
PA5403 523 tf

Warning: PA0487 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
3268 3.90e+00 ATAATcGggCGctct
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3269 1.20e+04 aaTgcgtgatccGaaAtAaTC
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3860 2.40e+04 aTTcCTC.TtT
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3861 4.30e+04 GTTGTTctGGG.GAt
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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 PA0487

PA0487 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
N-terminal domain of molybdenum-binding protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdate ion transport go/ biological_process
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
ModE_repress tigr/ tigrfam
Module neighborhood information for PA0487

PA0487 has total of 65 gene neighbors in modules 220, 523
Gene neighbors (65)
Gene Common Name Description Module membership
PA0168 PA0168 hypothetical protein (NCBI) 220, 316
PA0243 PA0243 probable transcriptional regulator (NCBI) 72, 220
PA0308 PA0308 hypothetical protein (NCBI) 220, 490
PA0351 PA0351 hypothetical protein (NCBI) 72, 220
PA0433 PA0433 hypothetical protein (NCBI) 187, 220
PA0446 PA0446 hypothetical protein (NCBI) 141, 523
PA0447 gcdH glutaryl-CoA dehydrogenase (NCBI) 185, 523
PA0479 PA0479 probable transcriptional regulator (NCBI) 397, 523
PA0487 PA0487 probable molybdenum transport regulator (NCBI) 220, 523
PA0538 dsbB disulfide bond formation protein (NCBI) 220, 498
PA0657 PA0657 probable ATPase (NCBI) 443, 523
PA0784 PA0784 probable transcriptional regulator (NCBI) 523, 551
PA0840 PA0840 probable oxidoreductase (NCBI) 523, 550
PA0846 PA0846 putative sulfate transport protein CysZ (NCBI) 117, 220
PA0847 PA0847 hypothetical protein (NCBI) 241, 523
PA0868 PA0868 hypothetical protein (NCBI) 72, 220
PA0946 PA0946 hypothetical protein (NCBI) 123, 220
PA1033 PA1033 probable glutathione S-transferase (NCBI) 462, 523
PA1047 PA1047 probable esterase (NCBI) 220, 420
PA1204 PA1204 hypothetical protein (NCBI) 338, 523
PA1205 PA1205 hypothetical protein (NCBI) 258, 523
PA1292 PA1292 probable 3-mercaptopyruvate sulfurtransferase (NCBI) 462, 523
PA1315 PA1315 probable transcriptional regulator (NCBI) 220, 438
PA1357 PA1357 hypothetical protein (NCBI) 72, 220
PA1398 PA1398 hypothetical protein (NCBI) 220, 229
PA1558 PA1558 hypothetical protein (NCBI) 220, 457
PA1618 PA1618 hypothetical protein (NCBI) 397, 523
PA1862 modB molybdenum transport protein ModB (NCBI) 220, 263
PA2035 PA2035 acetolactate synthase II large subunit (NCBI) 397, 523
PA2197 PA2197 hypothetical protein (NCBI) 389, 523
PA2198 PA2198 hypothetical protein (NCBI) 389, 523
PA2577 PA2577 probable transcriptional regulator (NCBI) 397, 523
PA2705 PA2705 hypothetical protein (NCBI) 7, 523
PA2823 PA2823 hypothetical protein (NCBI) 220, 315
PA2832 tpm thiopurine methyltransferase (NCBI) 70, 220
PA3004 PA3004 purine nucleoside phosphorylase (NCBI) 165, 220
PA3033 PA3033 hypothetical protein (NCBI) 117, 220
PA3034 PA3034 probable transcriptional regulator (NCBI) 41, 220
PA3127 PA3127 hypothetical protein (NCBI) 10, 523
PA3427 PA3427 probable short-chain dehydrogenases (NCBI) 397, 523
PA3757 PA3757 probable transcriptional regulator (NCBI) 397, 523
PA3758 PA3758 probable N-acetylglucosamine-6-phosphate deacetylase (NCBI) 397, 523
PA3759 PA3759 probable aminotransferase (NCBI) 295, 523
PA3760 PA3760 probable phosphotransferase protein (NCBI) 373, 523
PA3761 PA3761 probable phosphotransferase system protein (NCBI) 24, 523
PA3855 PA3855 hypothetical protein (NCBI) 220, 268
PA3859 PA3859 carboxylesterase (NCBI) 220, 225
PA3887 nhaP Na+/H+ antiporter NhaP (NCBI) 220, 490
PA3895 PA3895 probable transcriptional regulator (NCBI) 220, 268
PA3896 PA3896 probable 2-hydroxyacid dehydrogenase (NCBI) 220, 374
PA3970 amn AMP nucleosidase (NCBI) 378, 523
PA4026 PA4026 probable acetyltransferase (NCBI) 51, 523
PA4115 PA4115 hypothetical protein (NCBI) 378, 523
PA4282 PA4282 probable exonuclease (NCBI) 443, 523
PA4339 PA4339 probable phospholipase (NCBI) 20, 220
PA4472 pmbA PmbA protein (NCBI) 28, 523
PA4548 PA4548 probable D-amino acid oxidase (NCBI) 8, 220
PA4798 PA4798 hypothetical protein (NCBI) 511, 523
PA4976 aspC aspartate transaminase (NCBI) 397, 523
PA5085 PA5085 probable transcriptional regulator (NCBI) 220, 266
PA5175 cysQ CysQ protein (NCBI) 220, 321
PA5195 PA5195 probable heat shock protein (NCBI) 165, 523
PA5199 envZ two-component sensor EnvZ (NCBI) 220, 253
PA5370 PA5370 probable major facilitator superfamily (MFS) transporter (NCBI) 58, 220
PA5529 PA5529 probable sodium/proton antiporter (NCBI) 220, 422
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 PA0487
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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