Organism : Pseudomonas aeruginosa | Module List :
PA1285

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1285
(Mouseover regulator name to see its description)

PA1285 is regulated by 33 influences and regulates 9 modules.
Regulators for PA1285 (33)
Regulator Module Operator
PA0037 229 tf
PA0514 229 tf
PA0828 229 tf
PA1141 229 tf
PA1184 229 tf
PA1285 229 tf
PA1359 229 tf
PA1853 229 tf
PA2020 229 tf
PA2115 229 tf
PA2802 229 tf
PA2859 229 tf
PA3266 229 tf
PA3322 229 tf
PA3604 229 tf
PA4145 229 tf
PA4769 229 tf
PA0163 408 tf
PA0191 408 tf
PA0393 408 tf
PA0701 408 tf
PA1261 408 tf
PA1980 408 tf
PA3133 408 tf
PA3381 408 tf
PA3420 408 tf
PA3711 408 tf
PA3771 408 tf
PA3776 408 tf
PA4169 408 tf
PA5032 408 tf
PA5293 408 tf
PA5431 408 tf

Warning: PA1285 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
3286 1.50e+02 CgGgTAGAATgccCGcC.cTc
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3287 1.00e+03 agGc.gtACactGgGCg
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3640 3.10e-03 cCggcgCccg.CCacCCaccGc.g
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3641 4.80e+02 CCGGtgTCcGgcCttggcAGGGgC
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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 PA1285

PA1285 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1285

PA1285 has total of 59 gene neighbors in modules 229, 408
Gene neighbors (59)
Gene Common Name Description Module membership
PA0274 PA0274 hypothetical protein (NCBI) 330, 408
PA0419 PA0419 hypothetical protein (NCBI) 229, 247
PA0557 PA0557 hypothetical protein (NCBI) 24, 408
PA0560 PA0560 hypothetical protein (NCBI) 229, 375
PA0702 PA0702 hypothetical protein (NCBI) 23, 408
PA0845 PA0845 hypothetical protein (NCBI) 310, 408
PA0948 PA0948 hypothetical protein (NCBI) 214, 229
PA0951 PA0951 probable ribonuclease (NCBI) 229, 253
PA0995 ogt methylated-DNA--protein-cysteinemethyltransferase (NCBI) 30, 229
PA1075 PA1075 hypothetical protein (NCBI) 139, 229
PA1139 PA1139 hypothetical protein (NCBI) 187, 229
PA1141 PA1141 probable transcriptional regulator (NCBI) 68, 229
PA1222 PA1222 probable membrane-bound lytic murein transglycolase A (NCBI) 62, 229
PA1254 PA1254 probable dihydrodipicolinate synthetase (NCBI) 24, 408
PA1258 PA1258 probable permease of ABC transporter (NCBI) 50, 408
PA1259 PA1259 hypothetical protein (NCBI) 24, 408
PA1261 PA1261 probable transcriptional regulator (NCBI) 20, 408
PA1262 PA1262 probable major facilitator superfamily (MFS) transporter (NCBI) 267, 408
PA1284 PA1284 probable acyl-CoA dehydrogenase (NCBI) 408, 489
PA1285 PA1285 probable transcriptional regulator (NCBI) 229, 408
PA1286 PA1286 probable major facilitator superfamily (MFS) transporter (NCBI) 71, 408
PA1316 PA1316 probable major facilitator superfamily (MFS) transporter (NCBI) 408, 438
PA1398 PA1398 hypothetical protein (NCBI) 220, 229
PA1594 PA1594 hypothetical protein (NCBI) 229, 299
PA1645 PA1645 hypothetical protein (NCBI) 229, 457
PA1686 alkA DNA-3-methyladenine glycosidase II (NCBI) 189, 229
PA1848 PA1848 probable major facilitator superfamily (MFS) transporter (NCBI) 408, 434
PA1849 PA1849 hypothetical protein (NCBI) 335, 408
PA1962 acpD acyl carrier protein phosphodiesterase (NCBI) 323, 408
PA2061 PA2061 probable ATP-binding component of ABC transporter (NCBI) 12, 408
PA2568 PA2568 hypothetical protein (NCBI) 139, 229
PA2669 PA2669 hypothetical protein (NCBI) 71, 408
PA2670 PA2670 hypothetical protein (NCBI) 71, 408
PA2695 PA2695 hypothetical protein (NCBI) 229, 245
PA2773 PA2773 hypothetical protein (NCBI) 229, 445
PA2860 PA2860 hypothetical protein (NCBI) 229, 245
PA2911 PA2911 probable TonB-dependent receptor (NCBI) 83, 408
PA2912 PA2912 probable ATP-binding component of ABC transporter (NCBI) 83, 408
PA2914 PA2914 probable permease of ABC transporter (NCBI) 83, 408
PA2922 PA2922 probable hydrolase (NCBI) 408, 481
PA3130 PA3130 hypothetical protein (NCBI) 229, 313
PA3131 PA3131 probable aldolase (NCBI) 178, 229
PA3178 PA3178 hypothetical protein (NCBI) 229, 245
PA3288 PA3288 hypothetical protein (NCBI) 229, 313
PA3463 PA3463 hypothetical protein (NCBI) 72, 229
PA3595 PA3595 probable major facilitator superfamily (MFS) transporter (NCBI) 408, 425
PA3958 PA3958 hypothetical protein (NCBI) 229, 249
PA3960 PA3960 hypothetical protein (NCBI) 175, 408
PA3968 PA3968 probable pseudouridine synthase (NCBI) 86, 229
PA4075 PA4075 hypothetical protein (NCBI) 229, 422
PA4637 PA4637 hypothetical protein (NCBI) 139, 229
PA4718 PA4718 hypothetical protein (NCBI) 139, 229
PA4783 PA4783 hypothetical protein (NCBI) 101, 229
PA4789 PA4789 hypothetical protein (NCBI) 229, 351
PA4790 PA4790 hypothetical protein (NCBI) 229, 351
PA5019 PA5019 hypothetical protein (NCBI) 143, 229
PA5228 PA5228 hypothetical protein (NCBI) 109, 229
PA5259 hemD uroporphyrinogen-III synthetase (NCBI) 229, 296
PA5485 PA5485 hypothetical protein (NCBI) 126, 229
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 PA1285
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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