Organism : Pseudomonas aeruginosa | Module List :
PA2931

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2931
(Mouseover regulator name to see its description)

PA2931 is regulated by 22 influences and regulates 7 modules.
Regulators for PA2931 (22)
Regulator Module Operator
PA0791 246 tf
PA1235 246 tf
PA1351 246 tf
PA1399 246 tf
PA1945 246 tf
PA3594 246 tf
PA4021 246 tf
PA4052 246 tf
PA4341 246 tf
PA5389 246 tf
PA5438 246 tf
PA0652 79 tf
PA1283 79 tf
PA1539 79 tf
PA2054 79 tf
PA2825 79 tf
PA2849 79 tf
PA2931 79 tf
PA4270 79 tf
PA5059 79 tf
PA5337 79 tf
PA5344 79 tf

Warning: PA2931 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
2990 1.30e-12 ccat....cagAccgAtaacTa.A
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2991 1.10e-02 aTAgcGaCCgAtAccGgTtTttta
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3320 2.40e-07 CcgGcCggtctcg.AaGcaaaaaa
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3321 4.20e-05 aAA.TtaTggTt.TCgaTaaAcct
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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 PA2931

PA2931 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA2931

PA2931 has total of 53 gene neighbors in modules 79, 246
Gene neighbors (53)
Gene Common Name Description Module membership
PA0345 PA0345 hypothetical protein (NCBI) 246, 355
PA0742 PA0742 hypothetical protein (NCBI) 246, 489
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
PA0817 PA0817 probable ring-cleaving dioxygenase (NCBI) 163, 246
PA0841 PA0841 hypothetical protein (NCBI) 246, 373
PA1283 PA1283 probable transcriptional regulator (NCBI) 79, 432
PA1411 PA1411 hypothetical protein (NCBI) 246, 507
PA1525 alkB2 alkane-1-monooxygenase 2 (NCBI) 246, 288
PA1537 PA1537 probable short-chain dehydrogenase (NCBI) 79, 140
PA1538 PA1538 probable flavin-containing monooxygenase (NCBI) 79, 140
PA1539 PA1539 hypothetical protein (NCBI) 79, 140
PA1641 PA1641 hypothetical protein (NCBI) 79, 547
PA1851 PA1851 hypothetical protein (NCBI) 79, 461
PA1858 str streptomycin 3''-phosphotransferase (NCBI) 246, 295
PA2027 PA2027 hypothetical protein (NCBI) 79, 507
PA2052 cynS cyanate hydratase (NCBI) 79, 288
PA2053 cynT carbonate dehydratase (NCBI) 79, 288
PA2054 cynR transcriptional regulator CynR (NCBI) 79, 288
PA2096 PA2096 probable transcriptional regulator (NCBI) 246, 534
PA2097 PA2097 probable flavin-binding monooxygenase (NCBI) 246, 534
PA2098 PA2098 probable esterase/deacetylase (NCBI) 246, 534
PA2099 PA2099 short chain dehydrogenase (NCBI) 246, 534
PA2506 PA2506 hypothetical protein (NCBI) 79, 418
PA2825 PA2825 probable transcriptional regulator (NCBI) 79, 320
PA2826 PA2826 probable glutathione peroxidase (NCBI) 79, 376
PA2849 PA2849 probable transcriptional regulator (NCBI) 79, 243
PA2863 lipH lipase chaperone (NCBI) 246, 489
PA2886 PA2886 hypothetical protein (NCBI) 79, 330
PA2887 PA2887 probable short-chain dehydrogenase (NCBI) 79, 330
PA2888 PA2888 probable biotin-dependent carboxylase (NCBI) 79, 330
PA2890 PA2890 probable enoyl-CoA hydratase/isomerase (NCBI) 79, 330
PA2891 PA2891 probable biotin carboxylase/biotin carboxyl carrier protein (NCBI) 79, 330
PA2892 PA2892 short chain dehydrogenase (NCBI) 79, 330
PA2931 PA2931 probable transcriptional regulator (NCBI) 79, 246
PA2932 morB morphinone reductase (NCBI) 79, 246
PA2933 PA2933 probable major facilitator superfamily (MFS) transporter (NCBI) 246, 418
PA3024 PA3024 probable carbohydrate kinase (NCBI) 246, 489
PA3025 PA3025 probable FAD-dependent glycerol-3-phosphate dehydrogenase (NCBI) 246, 489
PA3860 PA3860 acyl-CoA synthase (NCBI) 104, 246
PA3865 PA3865 probable amino acid binding protein (NCBI) 79, 376
PA4337 PA4337 hypothetical protein (NCBI) 246, 483
PA4520 PA4520 probable chemotaxis transducer (NCBI) 79, 309
PA4589 PA4589 probable outer membrane protein precursor (NCBI) 246, 471
PA4603 PA4603 hypothetical protein (NCBI) 246, 483
PA4803 PA4803 hypothetical protein (NCBI) 79, 418
PA5205 PA5205 hypothetical protein (NCBI) 246, 473
PA5234 PA5234 probable oxidoreductase (NCBI) 79, 246
PA5433 PA5433 hypothetical protein (NCBI) 246, 497
PA5544 PA5544 hypothetical protein (NCBI) 246, 483
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 PA2931
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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