Organism : Pseudomonas aeruginosa | Module List :
PA1153

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Prophage antirepressor cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1153
(Mouseover regulator name to see its description)

PA1153 is regulated by 28 influences and regulates 12 modules.
Regulators for PA1153 (28)
Regulator Module Operator
PA0701 241 tf
PA1153 241 tf
PA1223 241 tf
PA1261 241 tf
PA2005 241 tf
PA2050 241 tf
PA3381 241 tf
PA3433 241 tf
PA4341 241 tf
PA4914 241 tf
PA5032 241 tf
PA5431 241 tf
PA1097 104 tf
PA1153 104 tf
PA1196 104 tf
PA2586 104 tf
PA2696 104 tf
PA2838 104 tf
PA3364 104 tf
PA3381 104 tf
PA3574 104 tf
PA3594 104 tf
PA3921 104 tf
PA4341 104 tf
PA4745 104 tf
PA4769 104 tf
PA4914 104 tf
PA5288 104 tf

Warning: PA1153 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
3040 2.10e-11 aACAAgAAac
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3041 7.60e+03 AcCacgActTtCcgTTgCA.t
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3310 3.80e+04 CGgaTaccCCAGatactC.CG
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3311 2.80e+04 AcGccT.TCctCacTG
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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 PA1153

PA1153 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Prophage antirepressor cog/ cog
Module neighborhood information for PA1153

PA1153 has total of 47 gene neighbors in modules 104, 241
Gene neighbors (47)
Gene Common Name Description Module membership
PA0229 pcaT dicarboxylic acid transporter PcaT (NCBI) 104, 432
PA0602 PA0602 probable binding protein component of ABC transporter (NCBI) 31, 241
PA0695 PA0695 hypothetical protein (NCBI) 104, 400
PA0697 PA0697 hypothetical protein (NCBI) 104, 400
PA0699 PA0699 probable peptidyl-prolyl cis-trans isomerase, PpiC-type (NCBI) 104, 400
PA0714 PA0714 hypothetical protein (NCBI) 241, 311
PA0751 PA0751 hypothetical protein (NCBI) 104, 246
PA0752 PA0752 hypothetical protein (NCBI) 104, 246
PA0753 PA0753 hypothetical protein (NCBI) 104, 246
PA0754 PA0754 hypothetical protein (NCBI) 104, 246
PA0755 PA0755 probable porin (NCBI) 104, 246
PA0847 PA0847 hypothetical protein (NCBI) 241, 523
PA1046 PA1046 hypothetical protein (NCBI) 241, 375
PA1133 PA1133 hypothetical protein (NCBI) 171, 241
PA1153 PA1153 hypothetical protein (NCBI) 104, 241
PA1169 PA1169 probable lipoxygenase (NCBI) 104, 473
PA1234 PA1234 hypothetical protein (NCBI) 20, 241
PA1409 aphA acetylpolyamine aminohydrolase (NCBI) 104, 425
PA1410 PA1410 probable periplasmic spermidine/putrescine-binding protein (NCBI) 104, 156
PA1636 kdpD two-component sensor KdpD (NCBI) 241, 313
PA1637 kdpE two-component response regulator KdpE (NCBI) 241, 313
PA2003 bdhA 3-hydroxybutyrate dehydrogenase (NCBI) 104, 365
PA2004 PA2004 hypothetical protein (NCBI) 104, 365
PA2005 PA2005 probable transcriptional regulator (NCBI) 241, 489
PA2341 PA2341 probable ATP-binding component of ABC maltose/mannitol transporter (NCBI) 104, 475
PA2507 catA catechol 1,2-dioxygenase (NCBI) 104, 500
PA2508 catC muconolactone delta-isomerase (NCBI) 104, 500
PA2515 xylL cis-1,2-dihydroxycyclohexa-3,4-diene carboxylate dehydrogenase (NCBI) 104, 172
PA2525 PA2525 probable outer membrane protein precursor (NCBI) 104, 196
PA2596 PA2596 hypothetical protein (NCBI) 241, 497
PA2682 PA2682 hypothetical protein (NCBI) 104, 500
PA3358 PA3358 hypothetical protein (NCBI) 171, 241
PA3669 PA3669 hypothetical protein (NCBI) 104, 241
PA3670 PA3670 hypothetical protein (NCBI) 104, 241
PA3671 PA3671 probable permease of ABC transporter (NCBI) 104, 313
PA3783 PA3783 hypothetical protein (NCBI) 175, 241
PA3860 PA3860 acyl-CoA synthase (NCBI) 104, 246
PA3886 PA3886 hypothetical protein (NCBI) 187, 241
PA4093 PA4093 hypothetical protein (NCBI) 241, 489
PA4347 PA4347 hypothetical protein (NCBI) 241, 253
PA4921 PA4921 hypothetical protein (NCBI) 206, 241
PA5089 PA5089 hypothetical protein (NCBI) 241, 473
PA5265 PA5265 hypothetical protein (NCBI) 104, 197
PA5266 PA5266 hypothetical protein (NCBI) 104, 197
PA5283 PA5283 probable transcriptional regulator (NCBI) 241, 434
PA5444 PA5444 hypothetical protein (NCBI) 206, 241
PA5514 poxB probable beta-lactamase (NCBI) 241, 469
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 PA1153
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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