Organism : Pseudomonas aeruginosa | Module List :
PA4585 rtcA

RNA 3'-terminal-phosphate cyclase (NCBI)

CircVis
Functional Annotations (4)
Function System
RNA 3'-terminal phosphate cyclase cog/ cog
RNA-3'-phosphate cyclase activity go/ molecular_function
RNA processing go/ biological_process
RNA_3prim_cycl tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4585
(Mouseover regulator name to see its description)

PA4585 is regulated by 41 influences and regulates 0 modules.
Regulators for PA4585 rtcA (41)
Regulator Module Operator
PA0032 61 tf
PA0121 61 tf
PA0133 61 tf
PA0152 61 tf
PA0448 61 tf
PA0739 61 tf
PA0831 61 tf
PA1128 61 tf
PA1630 61 tf
PA3433 61 tf
PA3711 61 tf
PA4070 61 tf
PA4094 61 tf
PA4184 61 tf
PA4354 61 tf
PA5253 61 tf
PA0120 501 tf
PA0207 501 tf
PA0236 501 tf
PA0831 501 tf
PA0905 501 tf
PA1128 501 tf
PA1142 501 tf
PA1422 501 tf
PA1627 501 tf
PA2032 501 tf
PA2047 501 tf
PA2115 501 tf
PA2258 501 tf
PA2718 501 tf
PA3921 501 tf
PA4021 501 tf
PA4157 501 tf
PA4279 501 tf
PA4354 501 tf
PA4769 501 tf
PA4853 501 tf
PA4890 501 tf
PA5059 501 tf
PA5437 501 tf
PA5483 501 tf

Warning: PA4585 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
2954 1.90e-15 AcAAcAAtAA
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2955 1.50e-06 aAacaggaTat.aaTttacc
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3816 8.40e+01 TTTTTcaT
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3817 1.90e+02 GtatttccaggAA.G
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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 PA4585

PA4585 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
RNA 3'-terminal phosphate cyclase cog/ cog
RNA-3'-phosphate cyclase activity go/ molecular_function
RNA processing go/ biological_process
RNA_3prim_cycl tigr/ tigrfam
Module neighborhood information for PA4585

PA4585 has total of 45 gene neighbors in modules 61, 501
Gene neighbors (45)
Gene Common Name Description Module membership
PA0040 PA0040 hypothetical protein (NCBI) 265, 501
PA0119 PA0119 probable dicarboxylate transporter (NCBI) 61, 125
PA0121 PA0121 hypothetical protein (NCBI) 61, 441
PA0133 PA0133 probable transcriptional regulator (NCBI) 61, 68
PA0293 aguB N-carbamoylputrescine amidohydrolase (NCBI) 61, 138
PA0333 PA0333 hypothetical protein (NCBI) 61, 320
PA0706 cat chloramphenicol acetyltransferase (NCBI) 384, 501
PA0739 PA0739 probable transcriptional regulator (NCBI) 34, 61
PA0978 PA0978 hypothetical protein (NCBI) 61, 231
PA1019 mucK cis,cis-muconate transporter MucK (NCBI) 52, 61
PA1157 PA1157 probable two-component response regulator (NCBI) 501, 528
PA1628 PA1628 probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) 61, 192
PA1629 PA1629 probable enoyl-CoA hydratase/isomerase (NCBI) 61, 303
PA1630 PA1630 probable transcriptional regulator (NCBI) 61, 303
PA1631 PA1631 probable acyl-CoA dehydrogenase (NCBI) 61, 303
PA1791 PA1791 hypothetical protein (NCBI) 265, 501
PA1839 PA1839 hypothetical protein (NCBI) 299, 501
PA2660 PA2660 hypothetical protein (NCBI) 478, 501
PA2758 PA2758 probable transcriptional regulator (NCBI) 61, 108
PA2921 PA2921 probable transcriptional regulator (NCBI) 61, 351
PA3433 PA3433 probable transcriptional regulator (NCBI) 61, 536
PA3741 PA3741 hypothetical protein (NCBI) 404, 501
PA3850 PA3850 hypothetical protein (NCBI) 265, 501
PA4070 PA4070 probable transcriptional regulator (NCBI) 61, 108
PA4094 PA4094 probable transcriptional regulator (NCBI) 61, 321
PA4119 aph aminoglycoside 3'-phosphotransferase type IIb (NCBI) 65, 501
PA4136 PA4136 probable major facilitator superfamily (MFS) transporter (NCBI) 61, 226
PA4184 PA4184 probable transcriptional regulator (NCBI) 61, 536
PA4197 PA4197 probable two-component sensor (NCBI) 61, 366
PA4198 PA4198 acyl-CoA synthase (NCBI) 61, 366
PA4582 PA4582 hypothetical protein (NCBI) 61, 157
PA4583 PA4583 hypothetical protein (NCBI) 61, 501
PA4585 rtcA RNA 3'-terminal-phosphate cyclase (NCBI) 61, 501
PA4724 PA4724 glutamyl-tRNA synthetase (NCBI) 286, 501
PA4799 PA4799 hypothetical protein (NCBI) 61, 157
PA4800 PA4800 hypothetical protein (NCBI) 61, 501
PA4928 PA4928 hypothetical protein (NCBI) 207, 501
PA4952 PA4952 ribosome-associated GTPase (NCBI) 306, 501
PA4985 PA4985 hypothetical protein (NCBI) 61, 138
PA4986 PA4986 probable oxidoreductase (NCBI) 61, 138
PA4987 PA4987 probable transcriptional regulator (NCBI) 61, 138
PA5048 PA5048 probable nuclease (NCBI) 135, 501
PA5072 PA5072 probable chemotaxis transducer (NCBI) 48, 61
PA5120 PA5120 hypothetical protein (NCBI) 48, 501
PA5246 PA5246 hypothetical protein (NCBI) 61, 335
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 PA4585
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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