Organism : Pseudomonas aeruginosa | Module List :
PA1351

probable sigma-70 factor, ECF subfamily (NCBI)

CircVis
Functional Annotations (7)
Function System
Predicted RNA polymerase sigma factor containing a TPR repeat domain cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1351
(Mouseover regulator name to see its description)

PA1351 is regulated by 24 influences and regulates 71 modules.
Regulators for PA1351 (24)
Regulator Module Operator
PA0533 292 tf
PA1351 292 tf
PA3420 292 tf
PA4057 292 tf
PA4703 292 tf
PA4745 292 tf
PA4914 292 tf
PA5032 292 tf
PA5059 292 tf
PA0564 386 tf
PA0701 386 tf
PA1145 386 tf
PA1351 386 tf
PA1980 386 tf
PA2376 386 tf
PA2547 386 tf
PA2586 386 tf
PA3045 386 tf
PA3133 386 tf
PA3381 386 tf
PA3420 386 tf
PA3711 386 tf
PA3771 386 tf
PA5032 386 tf

Warning: PA1351 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
3412 9.70e-08 CgGaAAATcgCccgcTCgAtga
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3413 1.10e+00 cTcccggtctacaccaAtaA
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3596 7.50e-01 AAAgGCG
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3597 7.60e+01 ACCTTGAAGTCGACTTcAATCTTA
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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 PA1351

PA1351 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted RNA polymerase sigma factor containing a TPR repeat domain cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for PA1351

PA1351 has total of 38 gene neighbors in modules 292, 386
Gene neighbors (38)
Gene Common Name Description Module membership
PA0051 phzH potential phenazine-modifying enzyme (NCBI) 152, 292
PA0153 pcaH protocatechuate 3,4-dioxygenase, beta subunit (NCBI) 292, 536
PA0397 PA0397 probable cation efflux system protein (NCBI) 53, 292
PA0532 PA0532 hypothetical protein (NCBI) 74, 292
PA0533 PA0533 probable transcriptional regulator (NCBI) 292, 537
PA0540 PA0540 hypothetical protein (NCBI) 292, 498
PA0709 PA0709 hypothetical protein (NCBI) 288, 292
PA0885 PA0885 probable C4-dicarboxylate transporter (NCBI) 386, 428
PA1238 PA1238 probable outer membrane component of multidrug efflux pump (NCBI) 177, 386
PA1351 PA1351 probable sigma-70 factor, ECF subfamily (NCBI) 292, 386
PA1778 cobA uroporphyrin-III C-methyltransferase (NCBI) 344, 386
PA1779 PA1779 assimilatory nitrate reductase (NCBI) 344, 386
PA1780 nirD assimilatory nitrite reductase small subunit (NCBI) 311, 386
PA1781 nirB assimilatory nitrite reductase large subunit (NCBI) 386, 532
PA1785 PA1785 hypothetical protein (NCBI) 311, 386
PA1953 PA1953 hypothetical protein (NCBI) 12, 386
PA1994 PA1994 hypothetical protein (NCBI) 292, 469
PA2120 PA2120 hypothetical protein (NCBI) 292, 373
PA2716 PA2716 probable FMN oxidoreductase (NCBI) 334, 386
PA2719 PA2719 hypothetical protein (NCBI) 190, 386
PA3323 PA3323 hypothetical protein (NCBI) 292, 546
PA3342 PA3342 hypothetical protein (NCBI) 136, 292
PA3773 PA3773 hypothetical protein (NCBI) 386, 486
PA4435 PA4435 probable acyl-CoA dehydrogenase (NCBI) 292, 483
PA4680 PA4680 hypothetical protein (NCBI) 136, 292
PA4681 PA4681 hypothetical protein (NCBI) 136, 292
PA4682 PA4682 hypothetical protein (NCBI) 136, 292
PA4827 PA4827 arylamine N-acetyltransferase (NCBI) 292, 497
PA4828 PA4828 hypothetical protein (NCBI) 292, 497
PA4861 PA4861 probable ATP-binding component of ABC transporter (NCBI) 177, 386
PA4862 PA4862 probable ATP-binding component of ABC transporter (NCBI) 386, 507
PA4882 PA4882 hypothetical protein (NCBI) 148, 386
PA4883 PA4883 hypothetical protein (NCBI) 148, 386
PA4926 PA4926 hypothetical protein (NCBI) 53, 292
PA4927 PA4927 hypothetical protein (NCBI) 53, 292
PA4929 PA4929 hypothetical protein (NCBI) 159, 292
PA5292 pchP phosphorylcholine phosphatase (NCBI) 175, 292
PA5325 PA5325 hypothetical protein (NCBI) 292, 428
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 PA1351
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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