Organism : Pseudomonas aeruginosa | Module List :
PA0708

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 PA0708
(Mouseover regulator name to see its description)

PA0708 is regulated by 29 influences and regulates 17 modules.
Regulators for PA0708 (29)
Regulator Module Operator
PA0708 101 tf
PA1359 101 tf
PA1399 101 tf
PA1544 101 tf
PA1570 101 tf
PA1713 101 tf
PA2622 101 tf
PA2692 101 tf
PA2737 101 tf
PA2848 101 tf
PA2899 101 tf
PA3133 101 tf
PA3714 101 tf
PA3845 101 tf
PA4508 101 tf
PA5116 101 tf
PA0034 138 tf
PA0133 138 tf
PA0248 138 tf
PA0708 138 tf
PA0893 138 tf
PA1241 138 tf
PA1738 138 tf
PA2047 138 tf
PA2586 138 tf
PA3135 138 tf
PA4157 138 tf
PA4581 138 tf
PA5506 138 tf

Warning: PA0708 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
3034 5.70e-05 AtagAtaagtTttaattatTt
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3035 5.60e-01 AAtCGaTTTcTaAaA
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3106 6.60e-14 attgttaActaT.a..aaaAA
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3107 4.50e-12 aT.ttaAAAaAacaagatcAa
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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 PA0708

PA0708 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 PA0708

PA0708 has total of 52 gene neighbors in modules 101, 138
Gene neighbors (52)
Gene Common Name Description Module membership
PA0034 PA0034 probable two-component response regulator (NCBI) 138, 343
PA0117 PA0117 probable short chain dehydrogenase (NCBI) 138, 373
PA0118 PA0118 hypothetical protein (NCBI) 138, 373
PA0248 PA0248 probable transcriptional regulator (NCBI) 138, 157
PA0293 aguB N-carbamoylputrescine amidohydrolase (NCBI) 61, 138
PA0441 dht dihydropyrimidinase (NCBI) 138, 481
PA0486 PA0486 hypothetical protein (NCBI) 23, 101
PA0574 PA0574 hypothetical protein (NCBI) 58, 138
PA0708 PA0708 probable transcriptional regulator (NCBI) 101, 138
PA0874 PA0874 hypothetical protein (NCBI) 58, 101
PA0984 PA0984 colicin immunity protein (NCBI) 101, 231
PA1044 PA1044 hypothetical protein (NCBI) 101, 375
PA1110 PA1110 hypothetical protein (NCBI) 101, 375
PA1163 PA1163 probable glucosyl transferase (NCBI) 101, 326
PA1227 PA1227 hypothetical protein (NCBI) 101, 438
PA1241 PA1241 probable transcriptional regulator (NCBI) 138, 173
PA1367 PA1367 hypothetical protein (NCBI) 101, 335
PA1383 PA1383 hypothetical protein (NCBI) 101, 254
PA1570 PA1570 probable transcriptional regulator (NCBI) 101, 157
PA1690 pscU translocation protein in type III secretion (NCBI) 101, 218
PA1691 pscT translocation protein in type III secretion (NCBI) 101, 218
PA1702 PA1702 conserved hypothetical protein in type III secretion (NCBI) 101, 218
PA1704 pcrR transcriptional regulator protein PcrR (NCBI) 101, 218
PA1738 PA1738 probable transcriptional regulator (NCBI) 138, 196
PA1739 PA1739 probable oxidoreductase (NCBI) 138, 326
PA2692 PA2692 probable transcriptional regulator (NCBI) 101, 126
PA2749 endA DNA-specific endonuclease I (NCBI) 138, 299
PA2852 PA2852 hypothetical protein (NCBI) 101, 335
PA2929 PA2929 hypothetical protein (NCBI) 23, 101
PA3135 PA3135 probable transcriptional regulator (NCBI) 138, 255
PA3715 PA3715 hypothetical protein (NCBI) 101, 443
PA3869 PA3869 hypothetical protein (NCBI) 101, 326
PA4121 PA4121 hypothetical protein (NCBI) 138, 317
PA4157 PA4157 probable transcriptional regulator (NCBI) 138, 268
PA4355 PA4355 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 108
PA4508 PA4508 probable transcriptional regulator (NCBI) 44, 101
PA4581 rtcR transcriptional regulator RtcR (NCBI) 138, 173
PA4588 gdhA glutamate dehydrogenase (NCBI) 138, 309
PA4631 PA4631 hypothetical protein (NCBI) 138, 187
PA4783 PA4783 hypothetical protein (NCBI) 101, 229
PA4830 PA4830 hypothetical protein (NCBI) 28, 101
PA4831 PA4831 probable transcriptional regulator (NCBI) 28, 101
PA4985 PA4985 hypothetical protein (NCBI) 61, 138
PA4986 PA4986 probable oxidoreductase (NCBI) 61, 138
PA4987 PA4987 probable transcriptional regulator (NCBI) 61, 138
PA5030 PA5030 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 196
PA5445 PA5445 probable coenzyme A transferase (NCBI) 138, 189
PA5506 PA5506 hypothetical protein (NCBI) 138, 358
PA5507 PA5507 hypothetical protein (NCBI) 138, 358
PA5508 PA5508 probable glutamine synthetase (NCBI) 138, 358
PA5509 PA5509 hypothetical protein (NCBI) 138, 358
PA5510 PA5510 probable transporter (NCBI) 138, 358
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 PA0708
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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