Organism : Pseudomonas aeruginosa | Module List :
PA3174

probable transcriptional regulator (NCBI)

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

Cytoscape Web
Regulation information for PA3174
(Mouseover regulator name to see its description)

PA3174 is regulated by 24 influences and regulates 5 modules.
Regulators for PA3174 (24)
Regulator Module Operator
PA1241 173 tf
PA1539 173 tf
PA2586 173 tf
PA2848 173 tf
PA3133 173 tf
PA3174 173 tf
PA3714 173 tf
PA4080 173 tf
PA4203 173 tf
PA4493 173 tf
PA4581 173 tf
PA4600 173 tf
PA5032 173 tf
PA5253 173 tf
PA1145 140 tf
PA1184 140 tf
PA1539 140 tf
PA1945 140 tf
PA1980 140 tf
PA2586 140 tf
PA3133 140 tf
PA3174 140 tf
PA3420 140 tf
PA5032 140 tf

Warning: PA3174 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
3110 2.90e-12 aaaagtAtctAgaaaAaagtatAc
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3111 3.10e-03 A.cTcGgCTTcAcCcTGtag
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3174 9.80e-23 AaAaa.ttatg.caaaAatgtcaa
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3175 6.10e-04 AttCt.tc.g.attcAAtCaAC
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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 PA3174

PA3174 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA3174

PA3174 has total of 37 gene neighbors in modules 140, 173
Gene neighbors (37)
Gene Common Name Description Module membership
PA0823 PA0823 hypothetical protein (NCBI) 173, 323
PA0824 PA0824 hypothetical protein (NCBI) 173, 323
PA0825 PA0825 hypothetical protein (NCBI) 173, 323
PA0875 PA0875 hypothetical protein (NCBI) 173, 537
PA0876 PA0876 probable transcriptional regulator (NCBI) 173, 368
PA0924 PA0924 hypothetical protein (NCBI) 140, 173
PA0987 PA0987 hypothetical protein (NCBI) 173, 323
PA1145 PA1145 probable transcriptional regulator (NCBI) 68, 140
PA1184 PA1184 probable transcriptional regulator (NCBI) 140, 542
PA1185 PA1185 probable glutathione S-transferase (NCBI) 140, 334
PA1231 PA1231 hypothetical protein (NCBI) 71, 140
PA1240 PA1240 probable enoyl-CoA hydratase/isomerase (NCBI) 173, 346
PA1241 PA1241 probable transcriptional regulator (NCBI) 138, 173
PA1291 PA1291 hypothetical protein (NCBI) 173, 438
PA1359 PA1359 probable transcriptional regulator (NCBI) 139, 173
PA1427 PA1427 hypothetical protein (NCBI) 140, 340
PA1537 PA1537 probable short-chain dehydrogenase (NCBI) 79, 140
PA1538 PA1538 probable flavin-containing monooxygenase (NCBI) 79, 140
PA1539 PA1539 hypothetical protein (NCBI) 79, 140
PA2590 PA2590 hypothetical protein (NCBI) 173, 346
PA2610 PA2610 hypothetical protein (NCBI) 140, 546
PA2839 PA2839 hypothetical protein (NCBI) 140, 550
PA2938 PA2938 probable transporter (NCBI) 97, 140
PA3132 PA3132 probable hydrolase (NCBI) 140, 173
PA3133 PA3133 probable transcriptional regulator (NCBI) 140, 173
PA3174 PA3174 probable transcriptional regulator (NCBI) 140, 173
PA3175 PA3175 probable arginase family protein (NCBI) 140, 173
PA3176 gltS sodium/glutamate symporter GltS (NCBI) 140, 148
PA3835 PA3835 hypothetical protein (NCBI) 44, 173
PA3867 PA3867 probable DNA invertase (NCBI) 173, 313
PA4080 PA4080 probable response regulator (NCBI) 173, 323
PA4513 PA4513 probable oxidoreductase (NCBI) 173, 473
PA4581 rtcR transcriptional regulator RtcR (NCBI) 138, 173
PA4597 oprJ Multidrug efflux outer membrane protein OprJ precursor (NCBI) 125, 173
PA4598 mexD Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexD (NCBI) 125, 173
PA4599 mexC Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexC precursor (NCBI) 125, 173
PA4600 nfxB transcriptional regulator NfxB (NCBI) 125, 173
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 PA3174
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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