Organism : Pseudomonas aeruginosa | Module List :
PA3410

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 PA3410
(Mouseover regulator name to see its description)

PA3410 is regulated by 22 influences and regulates 13 modules.
Regulators for PA3410 (22)
Regulator Module Operator
PA0472 339 tf
PA0816 339 tf
PA1363 339 tf
PA2270 339 tf
PA3410 339 tf
PA3899 339 tf
PA4227 339 tf
PA4896 339 tf
PA0149 444 tf
PA0472 444 tf
PA0864 444 tf
PA1138 444 tf
PA1359 444 tf
PA1363 444 tf
PA1912 444 tf
PA2299 444 tf
PA3410 444 tf
PA3899 444 tf
PA3965 444 tf
PA4227 444 tf
PA4896 444 tf
PA5274 444 tf

Warning: PA3410 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
3504 7.10e-25 aTGAtAat.ATTttCATTagcatt
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3505 2.00e+00 AtgGATtCatatatGcgtttTgTG
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3708 2.30e-33 aaAtGa.Aat.aTTaTCAatta.a
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3709 1.60e-03 AaATATcCcTTTTccGacaaaGT
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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 PA3410

PA3410 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 PA3410

PA3410 has total of 32 gene neighbors in modules 339, 444
Gene neighbors (32)
Gene Common Name Description Module membership
PA0149 PA0149 probable sigma-70 factor, ECF subfamily (NCBI) 325, 444
PA0470 PA0470 probable hydroxamate-type ferrisiderophore receptor (NCBI) 163, 444
PA0471 PA0471 probable transmembrane sensor (NCBI) 325, 444
PA0929 PA0929 two-component response regulator (NCBI) 98, 339
PA0930 PA0930 two-component sensor (NCBI) 98, 339
PA0931 pirA ferric enterobactin receptor PirA (NCBI) 339, 444
PA1302 PA1302 probable heme utilization protein precursor (NCBI) 339, 444
PA1911 PA1911 probable transmembrane sensor (NCBI) 325, 444
PA1912 PA1912 probable sigma-70 factor, ECF subfamily (NCBI) 325, 444
PA2686 pfeR two-component response regulator PfeR (NCBI) 339, 444
PA2687 pfeS two-component sensor PfeS (NCBI) 339, 550
PA2688 pfeA Ferric enterobactin receptor, outer membrane protein PfeA precursor (NCBI) 175, 339
PA3407 hasAp heme acquisition protein HasAp (NCBI) 119, 444
PA3408 hasR Haem uptake outer membrane receptor HasR precursor (NCBI) 119, 444
PA3409 PA3409 probable transmembrane sensor (NCBI) 119, 339
PA3410 PA3410 probable sigma-70 factor, ECF subfamily (NCBI) 339, 444
PA3530 PA3530 hypothetical protein (NCBI) 325, 339
PA3899 PA3899 probable sigma-70 factor, ECF subfamily (NCBI) 325, 339
PA3900 PA3900 probable transmembrane sensor (NCBI) 119, 339
PA4155 PA4155 hypothetical protein (NCBI) 325, 339
PA4156 PA4156 probable TonB-dependent receptor (NCBI) 325, 339
PA4168 fpvB second ferric pyoverdine receptor FpvB (NCBI) 339, 444
PA4705 PA4705 hypothetical protein (NCBI) 339, 444
PA4706 PA4706 probable ATP-binding component of ABC transporter (NCBI) 339, 444
PA4707 PA4707 probable permease of ABC transporter (NCBI) 339, 444
PA4708 PA4708 hypothetical protein (NCBI) 339, 444
PA4709 PA4709 probable hemin degrading factor (NCBI) 339, 444
PA4710 phuR Haem/Haemoglobin uptake outer membrane receptor PhuR precursor (NCBI) 339, 444
PA4711 PA4711 hypothetical protein (NCBI) 339, 444
PA4895 PA4895 probable transmembrane sensor (NCBI) 339, 444
PA4896 PA4896 probable sigma-70 factor, ECF subfamily (NCBI) 325, 444
PA4897 PA4897 hypothetical protein (NCBI) 325, 444
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 PA3410
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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