Organism : Pseudomonas aeruginosa | Module List :
PA2896

probable sigma-70 factor, ECF subfamily (NCBI)

CircVis
Functional Annotations (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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 PA2896
(Mouseover regulator name to see its description)

PA2896 is regulated by 53 influences and regulates 35 modules.
Regulators for PA2896 (53)
Regulator Module Operator
PA0125 27 tf
PA0233 27 tf
PA0376 27 tf
PA0436 27 tf
PA0905 27 tf
PA0979 27 tf
PA1229 27 tf
PA1430 27 tf
PA1663 27 tf
PA2032 27 tf
PA2093 27 tf
PA2270 27 tf
PA2718 27 tf
PA2896 27 tf
PA3002 27 tf
PA3249 27 tf
PA3398 27 tf
PA3410 27 tf
PA3583 27 tf
PA3689 27 tf
PA3879 27 tf
PA4145 27 tf
PA4270 27 tf
PA4341 27 tf
PA4462 27 tf
PA4508 27 tf
PA4659 27 tf
PA4703 27 tf
PA4890 27 tf
PA5029 27 tf
PA5105 27 tf
PA5166 27 tf
PA5261 27 tf
PA5365 27 tf
PA5483 27 tf
PA5511 27 tf
PA5562 27 tf
PA0547 322 tf
PA0763 322 tf
PA0961 322 tf
PA1351 322 tf
PA1430 322 tf
PA1504 322 tf
PA2896 322 tf
PA3563 322 tf
PA3596 322 tf
PA3879 322 tf
PA4508 322 tf
PA4703 322 tf
PA4853 322 tf
PA5261 322 tf
PA5483 322 tf
PA5550 322 tf

Warning: PA2896 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
2890 4.10e-13 aTTGaTtTaaaAggATTTtattTT
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2891 9.80e+01 aAaAAcAA
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3470 2.70e+02 AttGaccGcGCtgaCCGGcAcAAc
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3471 1.00e+03 G.A.atCTCCtTt
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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 PA2896

PA2896 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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 PA2896

PA2896 has total of 36 gene neighbors in modules 27, 322
Gene neighbors (36)
Gene Common Name Description Module membership
PA0059 osmC osmotically inducible protein OsmC (NCBI) 322, 479
PA0355 pfpI protease PfpI (NCBI) 322, 479
PA0543 PA0543 hypothetical protein (NCBI) 27, 322
PA0737 PA0737 hypothetical protein (NCBI) 27, 407
PA1065 PA1065 hypothetical protein (NCBI) 27, 382
PA1111 PA1111 hypothetical protein (NCBI) 280, 322
PA1118 PA1118 hypothetical protein (NCBI) 27, 133
PA1404 PA1404 hypothetical protein (NCBI) 27, 194
PA2021 PA2021 hypothetical protein (NCBI) 322, 479
PA2145 PA2145 hypothetical protein (NCBI) 27, 221
PA2166 PA2166 hypothetical protein (NCBI) 27, 521
PA2176 PA2176 hypothetical protein (NCBI) 322, 479
PA2433 PA2433 hypothetical protein (NCBI) 322, 479
PA2747 PA2747 hypothetical protein (NCBI) 27, 166
PA2751 PA2751 hypothetical protein (NCBI) 27, 322
PA2777 PA2777 hypothetical protein (NCBI) 322, 479
PA2883 PA2883 hypothetical protein (NCBI) 27, 169
PA2894 PA2894 hypothetical protein (NCBI) 27, 457
PA2895 PA2895 hypothetical protein (NCBI) 27, 322
PA2896 PA2896 probable sigma-70 factor, ECF subfamily (NCBI) 27, 322
PA3023 PA3023 hypothetical protein (NCBI) 28, 322
PA3369 PA3369 hypothetical protein (NCBI) 27, 166
PA3370 PA3370 hypothetical protein (NCBI) 27, 166
PA3371 PA3371 hypothetical protein (NCBI) 27, 166
PA3451 PA3451 hypothetical protein (NCBI) 27, 166
PA3788 PA3788 hypothetical protein (NCBI) 27, 322
PA4311 PA4311 hypothetical protein (NCBI) 322, 492
PA4345 PA4345 hypothetical protein (NCBI) 28, 322
PA4738 PA4738 hypothetical protein (NCBI) 27, 166
PA4739 PA4739 hypothetical protein (NCBI) 27, 166
PA4785 PA4785 acetyl-CoA acetyltransferase (NCBI) 322, 504
PA4786 PA4786 short-chain dehydrogenase (NCBI) 28, 322
PA4877 PA4877 hypothetical protein (NCBI) 322, 479
PA4879 PA4879 hypothetical protein (NCBI) 28, 322
PA5481 PA5481 hypothetical protein (NCBI) 27, 166
PA5482 PA5482 hypothetical protein (NCBI) 27, 166
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 PA2896
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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