Organism : Pseudomonas aeruginosa | Module List :
PA0163

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0163
(Mouseover regulator name to see its description)

PA0163 is regulated by 34 influences and regulates 37 modules.
Regulators for PA0163 (34)
Regulator Module Operator
PA0163 438 tf
PA0448 438 tf
PA1128 438 tf
PA1309 438 tf
PA1315 438 tf
PA1374 438 tf
PA1627 438 tf
PA1853 438 tf
PA2047 438 tf
PA3067 438 tf
PA3133 438 tf
PA5342 438 tf
PA0159 344 tf
PA0163 344 tf
PA0191 344 tf
PA0652 344 tf
PA1380 344 tf
PA1836 344 tf
PA1853 344 tf
PA2047 344 tf
PA2050 344 tf
PA2276 344 tf
PA2316 344 tf
PA2492 344 tf
PA3045 344 tf
PA3266 344 tf
PA3711 344 tf
PA3815 344 tf
PA3830 344 tf
PA4354 344 tf
PA5166 344 tf
PA5253 344 tf
PA5437 344 tf
PA5562 344 tf
Regulated by PA0163 (37)
Module Residual Genes
23 0.55 28
24 0.47 27
30 0.52 26
47 0.47 14
113 0.45 13
116 0.27 15
121 0.40 9
132 0.44 22
144 0.45 12
156 0.44 25
158 0.39 16
177 0.45 21
201 0.42 20
235 0.48 24
266 0.51 24
267 0.48 26
309 0.57 24
311 0.46 22
326 0.53 28
333 0.50 27
335 0.54 33
344 0.48 21
359 0.44 21
362 0.48 23
372 0.52 24
374 0.55 31
378 0.51 18
390 0.51 20
408 0.48 25
412 0.48 18
434 0.51 28
438 0.52 29
476 0.42 19
481 0.46 19
485 0.35 15
500 0.44 17
539 0.28 12
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3514 2.80e-03 cgCCGAttAtcGAcAtga
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3515 2.10e-01 GaA.TCcATCcgtCtTtTTCC
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3696 1.90e-04 T.AGaa.acgTagCtAT.aTcATg
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3697 2.40e-03 cTgGCc.aGGAAgAA
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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 PA0163

PA0163 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA0163

PA0163 has total of 49 gene neighbors in modules 344, 438
Gene neighbors (49)
Gene Common Name Description Module membership
PA0163 PA0163 probable transcriptional regulator (NCBI) 344, 438
PA0378 mtgA monofunctional biosynthetic peptidoglycan transglycosylase (NCBI) 181, 438
PA0379 PA0379 hypothetical protein (NCBI) 387, 438
PA0448 PA0448 probable transcriptional regulator (NCBI) 175, 438
PA0736 PA0736 hypothetical protein (NCBI) 372, 438
PA1128 PA1128 probable transcriptional regulator (NCBI) 175, 438
PA1227 PA1227 hypothetical protein (NCBI) 101, 438
PA1291 PA1291 hypothetical protein (NCBI) 173, 438
PA1309 PA1309 probable transcriptional regulator (NCBI) 266, 438
PA1315 PA1315 probable transcriptional regulator (NCBI) 220, 438
PA1316 PA1316 probable major facilitator superfamily (MFS) transporter (NCBI) 408, 438
PA1360 PA1360 hypothetical protein (NCBI) 247, 344
PA1373 fabF2 3-oxoacyl-(acyl carrier protein) synthase (NCBI) 68, 438
PA1374 PA1374 hypothetical protein (NCBI) 68, 438
PA1425 PA1425 probable ATP-binding component of ABC transporter (NCBI) 335, 438
PA1450 PA1450 hypothetical protein (NCBI) 266, 344
PA1540 PA1540 hypothetical protein (NCBI) 344, 412
PA1541 PA1541 probable drug efflux transporter (NCBI) 344, 412
PA1577 PA1577 hypothetical protein (NCBI) 236, 344
PA1626 PA1626 probable major facilitator superfamily (MFS) transporter (NCBI) 236, 438
PA1627 PA1627 probable transcriptional regulator (NCBI) 306, 438
PA1652 PA1652 hypothetical protein (NCBI) 68, 438
PA1778 cobA uroporphyrin-III C-methyltransferase (NCBI) 344, 386
PA1779 PA1779 assimilatory nitrate reductase (NCBI) 344, 386
PA1790 PA1790 hypothetical protein (NCBI) 135, 344
PA1836 PA1836 probable transcriptional regulator (NCBI) 44, 344
PA1960 PA1960 hypothetical protein (NCBI) 245, 438
PA2243 pslM hypothetical protein (NCBI) 24, 344
PA2314 PA2314 probable major facilitator superfamily (MFS) transporter (NCBI) 304, 344
PA2315 PA2315 hypothetical protein (NCBI) 135, 344
PA2316 PA2316 probable transcriptional regulator (NCBI) 135, 344
PA2563 PA2563 probable sulfate transporter (NCBI) 438, 507
PA2847 PA2847 hypothetical protein (NCBI) 44, 344
PA2956 PA2956 hypothetical protein (NCBI) 344, 422
PA3065 PA3065 hypothetical protein (NCBI) 324, 438
PA3066 PA3066 hypothetical protein (NCBI) 324, 438
PA3067 PA3067 probable transcriptional regulator (NCBI) 324, 438
PA3129 PA3129 hypothetical protein (NCBI) 135, 438
PA3312 PA3312 probable 3-hydroxyisobutyrate dehydrogenase (NCBI) 196, 438
PA3663 PA3663 hypothetical protein (NCBI) 335, 344
PA3679 PA3679 hypothetical protein (NCBI) 335, 438
PA3680 PA3680 hypothetical protein (NCBI) 114, 438
PA4609 radA DNA repair protein RadA (NCBI) 306, 438
PA4612 PA4612 hypothetical protein (NCBI) 152, 344
PA4635 PA4635 hypothetical protein (NCBI) 344, 412
PA5412 PA5412 hypothetical protein (NCBI) 359, 438
PA5442 PA5442 hypothetical protein (NCBI) 266, 438
PA5468 PA5468 probable citrate transporter (NCBI) 344, 375
PA5469 PA5469 hypothetical protein (NCBI) 344, 375
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 PA0163
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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