Organism : Pseudomonas aeruginosa | Module List :
PA3771

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3771
(Mouseover regulator name to see its description)

PA3771 is regulated by 29 influences and regulates 24 modules.
Regulators for PA3771 (29)
Regulator Module Operator
PA0032 537 tf
PA0217 537 tf
PA0272 537 tf
PA0528 537 tf
PA0533 537 tf
PA1184 537 tf
PA1945 537 tf
PA2848 537 tf
PA3771 537 tf
PA3776 537 tf
PA4269 537 tf
PA4914 537 tf
PA5032 537 tf
PA5189 537 tf
PA0701 340 tf
PA0748 340 tf
PA1067 340 tf
PA1980 340 tf
PA2047 340 tf
PA3045 340 tf
PA3133 340 tf
PA3420 340 tf
PA3630 340 tf
PA3771 340 tf
PA3776 340 tf
PA4436 340 tf
PA5032 340 tf
PA5293 340 tf
PA5431 340 tf

Warning: PA3771 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
3506 1.70e-01 tTT.t.gTTgTTct
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3507 2.60e+02 cAgatgaTCGA
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3886 3.10e+03 aaTGAgaAaTT
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3887 8.60e+02 AtCgAcaaATtatT
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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 PA3771

PA3771 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA3771

PA3771 has total of 47 gene neighbors in modules 340, 537
Gene neighbors (47)
Gene Common Name Description Module membership
PA0030 PA0030 hypothetical protein (NCBI) 20, 340
PA0031 betC choline sulfatase (NCBI) 340, 461
PA0217 PA0217 probable transcriptional regulator (NCBI) 394, 537
PA0272 PA0272 probable transcriptional regulator (NCBI) 337, 537
PA0287 gpuP 3-guanidinopropionate transport protein (NCBI) 340, 481
PA0442 PA0442 hypothetical protein (NCBI) 171, 340
PA0528 PA0528 probable transcriptional regulator (NCBI) 346, 537
PA0533 PA0533 probable transcriptional regulator (NCBI) 292, 537
PA0748 PA0748 still frameshift probable transcriptional regulator (NCBI) 33, 340
PA0785 PA0785 probable acyl carrier protein phosphodiesterase (NCBI) 311, 537
PA0786 PA0786 probable transporter (NCBI) 92, 537
PA0787 PA0787 hypothetical protein (NCBI) 245, 537
PA0875 PA0875 hypothetical protein (NCBI) 173, 537
PA0886 PA0886 probable C4-dicarboxylate transporter (NCBI) 340, 526
PA1107 PA1107 hypothetical protein (NCBI) 23, 537
PA1113 PA1113 probable ATP-binding/permease fusion ABC transporter (NCBI) 175, 537
PA1232 PA1232 hypothetical protein (NCBI) 71, 340
PA1239 PA1239 hypothetical protein (NCBI) 346, 537
PA1312 PA1312 probable transcriptional regulator (NCBI) 192, 537
PA1426 PA1426 hypothetical protein (NCBI) 97, 340
PA1427 PA1427 hypothetical protein (NCBI) 140, 340
PA1449 flhB flagellar biosynthesis protein (NCBI) 461, 537
PA1568 PA1568 hypothetical protein (NCBI) 148, 340
PA1569 PA1569 probable major facilitator superfamily (MFS) transporter (NCBI) 340, 537
PA1740 PA1740 hypothetical protein (NCBI) 97, 340
PA1932 PA1932 probable hydroxylase molybdopterin-containing subunit (NCBI) 280, 537
PA1933 PA1933 probable hydroxylase large subunit (NCBI) 280, 537
PA2217 PA2217 probable aldehyde dehydrogenase (NCBI) 36, 340
PA2218 PA2218 hypothetical protein (NCBI) 373, 537
PA2791 PA2791 hypothetical protein (NCBI) 340, 385
PA2848 PA2848 probable transcriptional regulator (NCBI) 355, 537
PA3090 PA3090 hypothetical protein (NCBI) 498, 537
PA3094 PA3094 probable transcriptional regulator (NCBI) 157, 537
PA3184 PA3184 probable transcriptional regulator (NCBI) 358, 537
PA3630 PA3630 probable transcriptional regulator (NCBI) 340, 373
PA3771 PA3771 probable transcriptional regulator (NCBI) 340, 537
PA3776 PA3776 probable transcriptional regulator (NCBI) 346, 537
PA3926 PA3926 probable major facilitator superfamily (MFS) transporter (NCBI) 340, 359
PA3964 PA3964 hypothetical protein (NCBI) 24, 340
PA3991 PA3991 hypothetical protein (NCBI) 71, 340
PA4028 PA4028 hypothetical protein (NCBI) 119, 340
PA4382 PA4382 hypothetical protein (NCBI) 44, 537
PA4436 PA4436 probable transcriptional regulator (NCBI) 58, 340
PA4510 PA4510 hypothetical protein (NCBI) 321, 537
PA4914 PA4914 probable transcriptional regulator (NCBI) 397, 537
PA5032 PA5032 probable transcriptional regulator (NCBI) 340, 359
PA5326 PA5326 hypothetical protein (NCBI) 340, 481
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 PA3771
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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