Organism : Pseudomonas aeruginosa | Module List :
PA1197

NAD-dependent deacetylase (NCBI)

CircVis
Functional Annotations (6)
Function System
NAD-dependent protein deacetylases, SIR2 family cog/ cog
DNA binding go/ molecular_function
chromatin silencing complex go/ cellular_component
chromatin silencing go/ biological_process
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1197
(Mouseover regulator name to see its description)

PA1197 is regulated by 27 influences and regulates 13 modules.
Regulators for PA1197 (27)
Regulator Module Operator
PA0133 68 tf
PA0253 68 tf
PA0675 68 tf
PA1067 68 tf
PA1141 68 tf
PA1145 68 tf
PA1197 68 tf
PA1374 68 tf
PA1945 68 tf
PA2534 68 tf
PA2877 68 tf
PA3002 68 tf
PA4174 68 tf
PA4270 68 tf
PA4989 68 tf
PA0448 162 tf
PA0515 162 tf
PA0527 162 tf
PA1050 162 tf
PA1196 162 tf
PA2126 162 tf
PA2622 162 tf
PA3458 162 tf
PA3879 162 tf
PA3973 162 tf
PA4853 162 tf
PA5550 162 tf

Warning: PA1197 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
2968 6.70e-14 tacgtaT..tCAagaaa.tcg.ag
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2969 2.70e-06 tTtAtCCacgcCAAgga.Ga
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3152 2.90e-10 tTGAtcCaggtCAa
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3153 2.70e-01 TTaa..aAg.aTTaa
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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 PA1197

PA1197 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
NAD-dependent protein deacetylases, SIR2 family cog/ cog
DNA binding go/ molecular_function
chromatin silencing complex go/ cellular_component
chromatin silencing go/ biological_process
Amino sugar and nucleotide sugar metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for PA1197

PA1197 has total of 49 gene neighbors in modules 68, 162
Gene neighbors (49)
Gene Common Name Description Module membership
PA0133 PA0133 probable transcriptional regulator (NCBI) 61, 68
PA0200 PA0200 hypothetical protein (NCBI) 162, 429
PA0527 dnr transcriptional regulator Dnr (NCBI) 162, 225
PA0545 PA0545 hypothetical protein (NCBI) 162, 375
PA0675 PA0675 probable sigma-70 factor, ECF subfamily (NCBI) 68, 500
PA0749 PA0749 hypothetical protein (NCBI) 68, 266
PA1049 pdxH pyridoxamine 5'-phosphate oxidase (NCBI) 162, 225
PA1050 PA1050 hypothetical protein (NCBI) 162, 253
PA1066 PA1066 short chain dehydrogenase (NCBI) 68, 346
PA1067 PA1067 probable transcriptional regulator (NCBI) 68, 542
PA1076 PA1076 hypothetical protein (NCBI) 162, 416
PA1141 PA1141 probable transcriptional regulator (NCBI) 68, 229
PA1145 PA1145 probable transcriptional regulator (NCBI) 68, 140
PA1194 PA1194 probable amino acid permease (NCBI) 68, 132
PA1195 PA1195 hypothetical protein (NCBI) 68, 313
PA1196 PA1196 probable transcriptional regulator (NCBI) 68, 162
PA1197 PA1197 NAD-dependent deacetylase (NCBI) 68, 162
PA1198 PA1198 hypothetical protein (NCBI) 68, 551
PA1199 PA1199 probable lipoprotein (NCBI) 68, 551
PA1200 PA1200 hypothetical protein (NCBI) 68, 551
PA1373 fabF2 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 68, 438
PA1374 PA1374 hypothetical protein (NCBI) 68, 438
PA1414 PA1414 hypothetical protein (NCBI) 162, 416
PA1429 PA1429 probable cation-transporting P-type ATPase (NCBI) 21, 162
PA1578 PA1578 hypothetical protein (NCBI) 68, 483
PA1652 PA1652 hypothetical protein (NCBI) 68, 438
PA1945 PA1945 probable transcriptional regulator (NCBI) 68, 136
PA2126 PA2126 hypothetical protein (NCBI) 162, 321
PA2127 PA2127 hypothetical protein (NCBI) 162, 225
PA2534 PA2534 probable transcriptional regulator (NCBI) 68, 288
PA2535 PA2535 probable oxidoreductase (NCBI) 68, 359
PA2877 PA2877 probable transcriptional regulator (NCBI) 68, 100
PA2910 PA2910 hypothetical protein (NCBI) 68, 92
PA3054 PA3054 hypothetical protein (NCBI) 162, 225
PA3458 PA3458 probable transcriptional regulator (NCBI) 38, 162
PA3572 PA3572 hypothetical protein (NCBI) 162, 416
PA3672 PA3672 probable ATP-binding component of ABC transporter (NCBI) 68, 283
PA3839 PA3839 probable sodium:sulfate symporter (NCBI) 162, 225
PA3878 narX two-component sensor NarX (NCBI) 162, 225
PA3879 narL two-component response regulator NarL (NCBI) 38, 162
PA4174 PA4174 probable transcriptional regulator (NCBI) 68, 542
PA4235 bfrA bacterioferritin (NCBI) 162, 225
PA4357 PA4357 hypothetical protein (NCBI) 162, 553
PA4358 PA4358 probable ferrous iron transport protein (NCBI) 162, 553
PA4359 PA4359 hypothetical protein (NCBI) 162, 553
PA4610 PA4610 hypothetical protein (NCBI) 38, 162
PA4832 PA4832 probable short-chain dehydrogenase (NCBI) 68, 119
PA4844 PA4844 probable chemotaxis transducer (NCBI) 68, 74
PA4924 PA4924 hypothetical protein (NCBI) 68, 283
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 PA1197
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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