Organism : Pseudomonas aeruginosa | Module List :
PA5239 rho

transcription termination factor Rho (NCBI)

CircVis
Functional Annotations (11)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
ATP binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
ATP synthesis coupled proton transport go/ biological_process
proton-transporting two-sector ATPase complex go/ cellular_component
hydrogen ion transporting ATP synthase activity, rotational mechanism go/ molecular_function
proton-transporting ATPase activity, rotational mechanism go/ molecular_function
RNA degradation kegg/ kegg pathway
rho tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5239
(Mouseover regulator name to see its description)

PA5239 is regulated by 35 influences and regulates 35 modules.
Regulators for PA5239 rho (35)
Regulator Module Operator
PA0890 131 tf
PA1898 131 tf
PA2047 131 tf
PA2957 131 tf
PA3804 131 tf
PA3948 131 tf
PA4238 131 tf
PA4451 131 tf
PA4499 131 tf
PA4530 131 tf
PA4581 131 tf
PA5239 131 tf
PA5550 131 tf
PA5562 131 tf
PA0121 214 tf
PA0393 214 tf
PA0455 214 tf
PA0487 214 tf
PA0890 214 tf
PA1898 214 tf
PA2054 214 tf
PA2879 214 tf
PA2957 214 tf
PA3002 214 tf
PA3285 214 tf
PA3604 214 tf
PA3804 214 tf
PA4238 214 tf
PA4451 214 tf
PA4600 214 tf
PA4806 214 tf
PA5239 214 tf
PA5483 214 tf
PA5550 214 tf
PA5562 214 tf
Regulated by PA5239 (35)
Module Residual Genes
14 0.55 17
56 0.39 11
75 0.47 14
87 0.55 26
103 0.52 18
128 0.41 11
131 0.54 18
133 0.44 13
176 0.51 20
185 0.54 19
195 0.57 21
200 0.44 16
212 0.61 30
214 0.50 19
256 0.42 16
258 0.53 17
270 0.46 19
276 0.53 12
305 0.46 14
329 0.46 17
341 0.58 19
353 0.50 21
358 0.58 25
360 0.41 13
404 0.42 12
427 0.41 13
474 0.45 15
475 0.52 25
478 0.56 23
493 0.55 18
499 0.55 24
510 0.37 10
515 0.44 18
549 0.43 9
552 0.48 13
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3092 5.60e-05 AaaAtA
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3093 2.70e-01 CAgtaaaGcctgAcAGaa.aActA
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3256 3.40e+00 ctT.ccccac.tCcT
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3257 2.10e+03 gTaGaATg.ccggCa
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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 PA5239

PA5239 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
ATP binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
ATP synthesis coupled proton transport go/ biological_process
proton-transporting two-sector ATPase complex go/ cellular_component
hydrogen ion transporting ATP synthase activity, rotational mechanism go/ molecular_function
proton-transporting ATPase activity, rotational mechanism go/ molecular_function
RNA degradation kegg/ kegg pathway
rho tigr/ tigrfam
Module neighborhood information for PA5239

PA5239 has total of 32 gene neighbors in modules 131, 214
Gene neighbors (32)
Gene Common Name Description Module membership
PA0783 putP sodium/proline symporter PutP (NCBI) 131, 315
PA0948 PA0948 hypothetical protein (NCBI) 214, 229
PA0949 wrbA Trp repressor binding protein WrbA (NCBI) 77, 214
PA0950 PA0950 probable arsenate reductase (NCBI) 77, 214
PA0956 proS prolyl-tRNA synthetase (NCBI) 214, 433
PA1543 apt adenine phosphoribosyltransferase (NCBI) 86, 214
PA1681 aroC chorismate synthase (NCBI) 214, 395
PA1682 PA1682 probable MFS metabolite transporter (NCBI) 214, 253
PA1683 PA1683 hypothetical protein (NCBI) 214, 511
PA1684 PA1684 probable oxidase (NCBI) 214, 378
PA3168 gyrA DNA gyrase subunit A (NCBI) 214, 395
PA3642 rnhB ribonuclease HII (NCBI) 131, 277
PA3650 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI) 131, 270
PA3827 PA3827 hypothetical protein (NCBI) 131, 353
PA4234 uvrA excinuclease ABC subunit A (NCBI) 131, 427
PA4250 rpsN 30S ribosomal protein S14 (NCBI) 131, 329
PA4427 sspB stringent starvation protein B (NCBI) 131, 212
PA4457 PA4457 hypothetical protein (NCBI) 131, 214
PA4498 PA4498 probable metallopeptidase (NCBI) 131, 517
PA4499 PA4499 probable transcriptional regulator (NCBI) 131, 212
PA4696 ilvI acetolactate synthase III large subunit (NCBI) 131, 543
PA4727 pcnB poly(A) polymerase (NCBI) 214, 270
PA5064 PA5064 hypothetical protein (NCBI) 214, 433
PA5190 PA5190 probable nitroreductase (NCBI) 131, 373
PA5239 rho transcription termination factor Rho (NCBI) 131, 214
PA5322 algC phosphomannomutase AlgC (NCBI) 91, 214
PA5323 argB acetylglutamate kinase (NCBI) 91, 214
PA5561 atpI ATP synthase subunit I (NCBI) 131, 354
PA5562 spoOJ chromosome partitioning protein Spo0J (NCBI) 82, 131
PA5563 soj chromosome partitioning protein Soj (NCBI) 131, 214
PA5564 gidB glucose-inhibited division protein B (NCBI) 131, 214
PA5565 gidA glucose-inhibited division protein A (NCBI) 131, 214
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 PA5239
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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