Organism : Pseudomonas aeruginosa | Module List :
PA4070

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (6)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4070
(Mouseover regulator name to see its description)

PA4070 is regulated by 25 influences and regulates 31 modules.
Regulators for PA4070 (25)
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
PA1003 108 tf
PA1484 108 tf
PA1633 108 tf
PA2320 108 tf
PA2484 108 tf
PA2488 108 tf
PA2758 108 tf
PA4070 108 tf
PA4354 108 tf
Regulated by PA4070 (31)
Module Residual Genes
5 0.34 16
33 0.54 23
34 0.57 34
35 0.51 19
47 0.47 14
52 0.37 18
61 0.56 31
86 0.59 20
91 0.52 20
108 0.52 24
137 0.40 13
146 0.45 20
174 0.48 16
215 0.53 19
226 0.64 16
233 0.42 13
234 0.56 27
276 0.53 12
298 0.21 15
319 0.39 20
329 0.46 17
336 0.50 19
341 0.58 19
361 0.53 23
365 0.49 22
433 0.44 16
441 0.51 18
451 0.51 15
506 0.32 9
552 0.48 13
553 0.37 19
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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3048 1.20e-28 aTagT..cTATCgAcagg..TgAT
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3049 8.80e-03 gttatc.aatCGAc.g.tcCgccc
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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 PA4070

PA4070 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Adenosine deaminase cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA4070

PA4070 has total of 53 gene neighbors in modules 61, 108
Gene neighbors (53)
Gene Common Name Description Module membership
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
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
PA1332 PA1332 hypothetical protein (NCBI) 108, 351
PA1333 PA1333 hypothetical protein (NCBI) 108, 361
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
PA1743 PA1743 hypothetical protein (NCBI) 108, 446
PA1744 PA1744 hypothetical protein (NCBI) 108, 326
PA1942 PA1942 hypothetical protein (NCBI) 9, 108
PA1970 PA1970 hypothetical protein (NCBI) 108, 226
PA2018 PA2018 RND multidrug efflux transporter (NCBI) 39, 108
PA2317 PA2317 probable oxidoreductase (NCBI) 108, 291
PA2493 mexE Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexE precursor (NCBI) 108, 494
PA2494 mexF Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexF (NCBI) 108, 494
PA2495 oprN Multidrug efflux outer membrane protein OprN precursor (NCBI) 108, 494
PA2758 PA2758 probable transcriptional regulator (NCBI) 61, 108
PA2759 PA2759 hypothetical protein (NCBI) 108, 291
PA2813 PA2813 probable glutathione S-transferase (NCBI) 9, 108
PA2921 PA2921 probable transcriptional regulator (NCBI) 61, 351
PA3229 PA3229 hypothetical protein (NCBI) 108, 291
PA3230 PA3230 hypothetical protein (NCBI) 108, 109
PA3433 PA3433 probable transcriptional regulator (NCBI) 61, 536
PA4070 PA4070 probable transcriptional regulator (NCBI) 61, 108
PA4094 PA4094 probable transcriptional regulator (NCBI) 61, 321
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
PA4353 PA4353 hypothetical protein (NCBI) 108, 461
PA4354 PA4354 hypothetical protein (NCBI) 108, 337
PA4355 PA4355 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 108
PA4356 xenB xenobiotic reductase (NCBI) 62, 108
PA4582 PA4582 hypothetical protein (NCBI) 61, 157
PA4583 PA4583 hypothetical protein (NCBI) 61, 501
PA4585 rtcA RNA 3'-terminal-phosphate cyclase (NCBI) 61, 501
PA4623 PA4623 hypothetical protein (NCBI) 108, 152
PA4799 PA4799 hypothetical protein (NCBI) 61, 157
PA4800 PA4800 hypothetical protein (NCBI) 61, 501
PA4881 PA4881 hypothetical protein (NCBI) 108, 152
PA4985 PA4985 hypothetical protein (NCBI) 61, 138
PA4986 PA4986 probable oxidoreductase (NCBI) 61, 138
PA4987 PA4987 probable transcriptional regulator (NCBI) 61, 138
PA5072 PA5072 probable chemotaxis transducer (NCBI) 48, 61
PA5246 PA5246 hypothetical protein (NCBI) 61, 335
PA5465 PA5465 hypothetical protein (NCBI) 70, 108
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 PA4070
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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