Organism : Pseudomonas aeruginosa | Module List :
PA3765

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3765
(Mouseover regulator name to see its description)

PA3765 is regulated by 22 influences and regulates 0 modules.
Regulators for PA3765 (22)
Regulator Module Operator
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
PA0179 157 tf
PA0248 157 tf
PA1570 157 tf
PA2586 157 tf
PA3133 157 tf
PA3921 157 tf
PA4120 157 tf
PA4238 157 tf

Warning: PA3765 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
3142 3.70e-16 CGATcaaTaaCatGttAtaTAtaA
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3143 1.90e-02 gAcgaaaggggcaGCcACagG
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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 PA3765

PA3765 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for PA3765

PA3765 has total of 51 gene neighbors in modules 157, 542
Gene neighbors (51)
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
PA0248 PA0248 probable transcriptional regulator (NCBI) 138, 157
PA0445 PA0445 probable transposase (NCBI) 157, 324
PA0477 PA0477 probable transcriptional regulator (NCBI) 536, 542
PA0478 PA0478 probable N-acetyltransferase (NCBI) 373, 542
PA0561 PA0561 hypothetical protein (NCBI) 157, 445
PA0669 dnaE2 error-prone DNA polymerase (RefSeq) 211, 542
PA0670 PA0670 hypothetical protein (NCBI) 468, 542
PA0671 PA0671 hypothetical protein (NCBI) 468, 542
PA0777 PA0777 hypothetical protein (NCBI) 157, 550
PA0821 PA0821 hypothetical protein (NCBI) 157, 231
PA0822 PA0822 hypothetical protein (NCBI) 157, 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
PA1378 PA1378 hypothetical protein (NCBI) 70, 157
PA1535 PA1535 probable acyl-CoA dehydrogenase (NCBI) 157, 330
PA1570 PA1570 probable transcriptional regulator (NCBI) 101, 157
PA1647 PA1647 probable sulfate transporter (NCBI) 333, 542
PA2542 PA2542 hypothetical protein (NCBI) 157, 313
PA2543 PA2543 hypothetical protein (NCBI) 157, 313
PA2752 PA2752 hypothetical protein (NCBI) 235, 542
PA3092 fadH1 2,4-dienoyl-CoA reductase FadH1 (NCBI) 157, 313
PA3093 PA3093 hypothetical protein (NCBI) 157, 320
PA3094 PA3094 probable transcriptional regulator (NCBI) 157, 537
PA3209 PA3209 hypothetical protein (NCBI) 157, 372
PA3223 acpD acyl carrier protein phosphodiesterase (NCBI) 206, 542
PA3367 PA3367 hypothetical protein (NCBI) 157, 372
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
PA4037 PA4037 probable ATP-binding component of ABC transporter (NCBI) 71, 542
PA4039 PA4039 hypothetical protein (NCBI) 71, 542
PA4120 PA4120 probable transcriptional regulator (NCBI) 157, 317
PA4122 PA4122 hypothetical protein (NCBI) 157, 317
PA4123 hpcC 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase (NCBI) 157, 317
PA4124 hpcB homoprotocatechuate 2,3-dioxygenase (NCBI) 157, 317
PA4125 hpcD 5-carboxymethyl-2-hydroxymuconate isomerase (NCBI) 157, 317
PA4126 PA4126 probable major facilitator superfamily (MFS) transporter (NCBI) 157, 317
PA4127 hpcG 2-oxo-hept-3-ene-1,7-dioate hydratase (NCBI) 157, 317
PA4128 PA4128 hypothetical protein (NCBI) 157, 317
PA4173 PA4173 hypothetical protein (NCBI) 288, 542
PA4174 PA4174 probable transcriptional regulator (NCBI) 68, 542
PA4582 PA4582 hypothetical protein (NCBI) 61, 157
PA4584 PA4584 hypothetical protein (NCBI) 39, 157
PA4691 PA4691 hypothetical protein (NCBI) 157, 521
PA4692 PA4692 hypothetical protein (NCBI) 157, 236
PA4799 PA4799 hypothetical protein (NCBI) 61, 157
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 PA3765
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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