Organism : Pseudomonas aeruginosa | Module List :
PA4039

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
ABC-type uncharacterized transport system involved in gliding motility, auxiliary component cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4039
(Mouseover regulator name to see its description)

PA4039 is regulated by 36 influences and regulates 0 modules.
Regulators for PA4039 (36)
Regulator Module Operator
PA0268 71 tf
PA0701 71 tf
PA0893 71 tf
PA1067 71 tf
PA1136 71 tf
PA1229 71 tf
PA1269 71 tf
PA1347 71 tf
PA2047 71 tf
PA2121 71 tf
PA2547 71 tf
PA3045 71 tf
PA3133 71 tf
PA3420 71 tf
PA3714 71 tf
PA3776 71 tf
PA4057 71 tf
PA4169 71 tf
PA4341 71 tf
PA5032 71 tf
PA5293 71 tf
PA5431 71 tf
PA0032 542 tf
PA0056 542 tf
PA0477 542 tf
PA0828 542 tf
PA1067 542 tf
PA1138 542 tf
PA1226 542 tf
PA3398 542 tf
PA3433 542 tf
PA3714 542 tf
PA4174 542 tf
PA5293 542 tf
PA5428 542 tf
PA5431 542 tf

Warning: PA4039 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
2974 7.20e-06 aTaAgtaatcgaTa.t.gaAaat
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2975 1.40e-02 CCtGTgcTTGTacGAA.tt.acta
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3896 6.70e-14 gaTtgtcgggattat.catacact
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3897 2.10e-03 GaTcagtcCaTcCt.GgGcgcctg
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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 PA4039

PA4039 is enriched for 1 functions in 3 categories.
Module neighborhood information for PA4039

PA4039 has total of 38 gene neighbors in modules 71, 542
Gene neighbors (38)
Gene Common Name Description Module membership
PA0032 PA0032 probable transcriptional regulator (NCBI) 346, 542
PA0056 PA0056 probable transcriptional regulator (NCBI) 346, 542
PA0069 PA0069 hypothetical protein (NCBI) 311, 542
PA0477 PA0477 probable transcriptional regulator (NCBI) 536, 542
PA0478 PA0478 probable N-acetyltransferase (NCBI) 373, 542
PA0669 dnaE2 error-prone DNA polymerase (RefSeq) 211, 542
PA0670 PA0670 hypothetical protein (NCBI) 468, 542
PA0671 PA0671 hypothetical protein (NCBI) 468, 542
PA0994 cupC3 usher CupC3 (NCBI) 71, 231
PA1067 PA1067 probable transcriptional regulator (NCBI) 68, 542
PA1184 PA1184 probable transcriptional regulator (NCBI) 140, 542
PA1225 PA1225 probable NAD(P)H dehydrogenase (NCBI) 92, 542
PA1226 PA1226 probable transcriptional regulator (NCBI) 507, 542
PA1229 PA1229 probable transcriptional regulator (NCBI) 71, 337
PA1230 PA1230 hypothetical protein (NCBI) 50, 71
PA1231 PA1231 hypothetical protein (NCBI) 71, 140
PA1232 PA1232 hypothetical protein (NCBI) 71, 340
PA1233 PA1233 hypothetical protein (NCBI) 71, 337
PA1286 PA1286 probable major facilitator superfamily (MFS) transporter (NCBI) 71, 408
PA1647 PA1647 probable sulfate transporter (NCBI) 333, 542
PA2669 PA2669 hypothetical protein (NCBI) 71, 408
PA2670 PA2670 hypothetical protein (NCBI) 71, 408
PA2752 PA2752 hypothetical protein (NCBI) 235, 542
PA2935 PA2935 hypothetical protein (NCBI) 24, 71
PA3223 acpD acyl carrier protein phosphodiesterase (NCBI) 206, 542
PA3398 PA3398 probable transcriptional regulator (NCBI) 536, 542
PA3765 PA3765 hypothetical protein (NCBI) 157, 542
PA3894 PA3894 probable outer membrane protein precursor (NCBI) 542, 545
PA3954 PA3954 hypothetical protein (NCBI) 71, 158
PA3991 PA3991 hypothetical protein (NCBI) 71, 340
PA4037 PA4037 probable ATP-binding component of ABC transporter (NCBI) 71, 542
PA4039 PA4039 hypothetical protein (NCBI) 71, 542
PA4173 PA4173 hypothetical protein (NCBI) 288, 542
PA4174 PA4174 probable transcriptional regulator (NCBI) 68, 542
PA4858 PA4858 hypothetical protein (NCBI) 71, 486
PA5341 PA5341 hypothetical protein (NCBI) 71, 333
PA5480 PA5480 hypothetical protein (NCBI) 71, 497
PA5566 PA5566 hypothetical protein (NCBI) 71, 119
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 PA4039
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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