Organism : Pseudomonas aeruginosa | Module List :
PA0701

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0701
(Mouseover regulator name to see its description)

PA0701 is regulated by 21 influences and regulates 59 modules.
Regulators for PA0701 (21)
Regulator Module Operator
PA0701 50 tf
PA0828 50 tf
PA1351 50 tf
PA1949 50 tf
PA1980 50 tf
PA2050 50 tf
PA2093 50 tf
PA2547 50 tf
PA2838 50 tf
PA3776 50 tf
PA4341 50 tf
PA5032 50 tf
PA5562 50 tf
PA0191 400 tf
PA0527 400 tf
PA0675 400 tf
PA0701 400 tf
PA0707 400 tf
PA2696 400 tf
PA3381 400 tf
PA5525 400 tf

Warning: PA0701 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
2932 2.40e+00 aTgttTT.tacAgAac.gttt
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2933 7.10e+02 cTggCGaAgaAatg
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3624 5.10e+01 aaagccccGcTccAgGgaCTTgc
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3625 1.20e+03 TGAcAaatctT
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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 PA0701

PA0701 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA0701

PA0701 has total of 30 gene neighbors in modules 50, 400
Gene neighbors (30)
Gene Common Name Description Module membership
PA0184 PA0184 probable ATP-binding component of ABC transporter (NCBI) 50, 362
PA0450 PA0450 probable phosphate transporter (NCBI) 25, 50
PA0474 PA0474 hypothetical protein (NCBI) 12, 50
PA0680 PA0680 HxcV putative pseudopilin (NCBI) 105, 400
PA0681 PA0681 HxcT pseudopilin (NCBI) 132, 400
PA0682 PA0682 HxcX atypical pseudopilin (NCBI) 132, 400
PA0683 PA0683 probable type II secretion system protein (NCBI) 132, 400
PA0684 PA0684 probable type II secretion system protein (NCBI) 132, 400
PA0685 PA0685 probable type II secretion system protein (NCBI) 158, 400
PA0686 PA0686 probable type II secretion system protein (NCBI) 158, 400
PA0687 PA0687 probable type II secretion system protein (NCBI) 132, 400
PA0690 PA0690 hypothetical protein (NCBI) 400, 532
PA0695 PA0695 hypothetical protein (NCBI) 104, 400
PA0696 PA0696 hypothetical protein (NCBI) 158, 400
PA0697 PA0697 hypothetical protein (NCBI) 104, 400
PA0698 PA0698 hypothetical protein (NCBI) 321, 400
PA0699 PA0699 probable peptidyl-prolyl cis-trans isomerase, PpiC-type (NCBI) 104, 400
PA0701 PA0701 probable transcriptional regulator (NCBI) 50, 400
PA1230 PA1230 hypothetical protein (NCBI) 50, 71
PA1257 PA1257 probable permease of ABC transporter (NCBI) 50, 330
PA1258 PA1258 probable permease of ABC transporter (NCBI) 50, 408
PA2057 PA2057 hypothetical protein (NCBI) 12, 50
PA2058 PA2058 probable binding protein component of ABC transporter (NCBI) 50, 132
PA2060 PA2060 probable permease of ABC transporter (NCBI) 12, 50
PA2835 PA2835 probable major facilitator superfamily (MFS) transporter (NCBI) 50, 486
PA3775 PA3775 hypothetical protein (NCBI) 12, 50
PA4193 PA4193 probable permease of ABC transporter (NCBI) 50, 301
PA4194 PA4194 probable permease of ABC transporter (NCBI) 50, 301
PA4905 vanB vanillate O-demethylase oxidoreductase (NCBI) 50, 177
PA4981 PA4981 probable amino acid permease (NCBI) 50, 330
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 PA0701
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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