Organism : Pseudomonas aeruginosa | Module List :
PA0905 rsmA

RsmA, regulator of secondary metabolites (NCBI)

CircVis
Functional Annotations (9)
Function System
Carbon storage regulator (could also regulate swarming and quorum sensing) cog/ cog
RNA binding go/ molecular_function
regulation of carbohydrate metabolic process go/ biological_process
mRNA metabolic process go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Two-component system kegg/ kegg pathway
csrA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0905
(Mouseover regulator name to see its description)

PA0905 is regulated by 24 influences and regulates 23 modules.
Regulators for PA0905 rsmA (24)
Regulator Module Operator
PA0436 57 tf
PA0905 57 tf
PA1159 57 tf
PA1455 57 tf
PA1754 57 tf
PA1760 57 tf
PA1776 57 tf
PA2586 57 tf
PA2737 57 tf
PA3133 57 tf
PA3458 57 tf
PA5253 57 tf
PA5288 57 tf
PA0179 525 tf
PA0376 525 tf
PA0763 525 tf
PA0905 525 tf
PA1142 525 tf
PA1754 525 tf
PA2622 525 tf
PA4315 525 tf
PA4764 525 tf
PA5253 525 tf
PA5288 525 tf

Warning: PA0905 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
2946 5.50e-01 CcagggtaAaCGccttGA.ct
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2947 4.40e+00 actGaactTTCgTgCCaTga
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3864 3.10e-05 tgCaaa.ggtTgctacgAa.aAtt
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3865 1.00e+03 AATACCCCTACAGGGTATCA
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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 PA0905

PA0905 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Carbon storage regulator (could also regulate swarming and quorum sensing) cog/ cog
RNA binding go/ molecular_function
regulation of carbohydrate metabolic process go/ biological_process
mRNA metabolic process go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Two-component system kegg/ kegg pathway
csrA tigr/ tigrfam
Module neighborhood information for PA0905

PA0905 has total of 35 gene neighbors in modules 57, 525
Gene neighbors (35)
Gene Common Name Description Module membership
PA0039 PA0039 hypothetical protein (NCBI) 279, 525
PA0436 PA0436 probable transcriptional regulator (NCBI) 57, 88
PA0905 rsmA RsmA, regulator of secondary metabolites (NCBI) 57, 525
PA1159 PA1159 probable cold-shock protein (NCBI) 57, 455
PA1592 PA1592 hypothetical protein (NCBI) 279, 525
PA1769 PA1769 hypothetical protein (NCBI) 57, 390
PA1776 sigX ECF sigma factor SigX (NCBI) 57, 195
PA1793 ppiB peptidyl-prolyl cis-trans isomerase B (NCBI) 57, 182
PA1802 clpX ATP-dependent protease ATP-binding subunit (NCBI) 57, 464
PA2586 gacA response regulator GacA (NCBI) 57, 513
PA2620 clpA ATP-binding protease component ClpA (NCBI) 10, 525
PA2621 clpS ATP-dependent Clp protease adaptor protein ClpS (RefSeq) 279, 525
PA2622 cspD cold-shock protein CspD (NCBI) 279, 525
PA2797 PA2797 hypothetical protein (NCBI) 57, 316
PA2805 PA2805 hypothetical protein (NCBI) 279, 525
PA2853 oprI Outer membrane lipoprotein OprI precursor (NCBI) 57, 525
PA3031 PA3031 hypothetical protein (NCBI) 273, 525
PA3385 amrZ alginate and motility regulator Z (NCBI) 455, 525
PA3752 PA3752 hypothetical protein (NCBI) 57, 488
PA3753 PA3753 hypothetical protein (NCBI) 57, 488
PA3754 PA3754 hypothetical protein (NCBI) 57, 488
PA3755 PA3755 hypothetical protein (NCBI) 41, 57
PA3756 PA3756 hypothetical protein (NCBI) 41, 57
PA4315 mvaT transcriptional regulator MvaT, P16 subunit (NCBI) 525, 551
PA4463 PA4463 hypothetical protein (NCBI) 15, 525
PA4466 PA4466 probable phosphoryl carrier protein (NCBI) 57, 75
PA4495 PA4495 hypothetical protein (NCBI) 525, 551
PA4614 mscL large-conductance mechanosensitive channel (NCBI) 279, 525
PA4735 PA4735 hypothetical protein (NCBI) 57, 203
PA4736 PA4736 hypothetical protein (NCBI) 57, 203
PA4737 PA4737 hypothetical protein (NCBI) 57, 203
PA5226 PA5226 hypothetical protein (NCBI) 57, 499
PA5253 algP alginate regulatory protein AlgP (NCBI) 15, 525
PA5288 glnK nitrogen regulatory protein P-II 2 (NCBI) 57, 525
PA5306 PA5306 hypothetical protein (NCBI) 57, 88
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 PA0905
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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