Organism : Pseudomonas aeruginosa | Module List :
PA0367

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0367
(Mouseover regulator name to see its description)

PA0367 is regulated by 22 influences and regulates 19 modules.
Regulators for PA0367 (22)
Regulator Module Operator
PA0791 189 tf
PA1283 189 tf
PA2020 189 tf
PA2196 189 tf
PA2312 189 tf
PA3133 189 tf
PA3721 189 tf
PA4052 189 tf
PA0167 338 tf
PA0367 338 tf
PA0393 338 tf
PA0784 338 tf
PA1159 338 tf
PA1315 338 tf
PA2047 338 tf
PA2246 338 tf
PA2267 338 tf
PA2492 338 tf
PA2718 338 tf
PA3714 338 tf
PA3921 338 tf
PA4787 338 tf

Warning: PA0367 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
3206 2.70e+05 AAGGAA
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3207 1.30e+04 GGtgtGgCGg.tgGAa.gtggGc
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3502 8.40e+03 cC.AcAAcaA.
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3503 7.50e+03 ctGAacgAcAa
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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 PA0367

PA0367 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA0367

PA0367 has total of 64 gene neighbors in modules 189, 338
Gene neighbors (64)
Gene Common Name Description Module membership
PA0327 PA0327 hypothetical protein (NCBI) 171, 189
PA0367 PA0367 probable transcriptional regulator (NCBI) 189, 338
PA0568 PA0568 hypothetical protein (NCBI) 23, 189
PA0570 PA0570 hypothetical protein (NCBI) 23, 189
PA0603 PA0603 probable ATP-binding component of ABC transporter (NCBI) 234, 338
PA0604 PA0604 probable binding protein component of ABC transporter (NCBI) 234, 338
PA0658 PA0658 probable short-chain dehydrogenase (NCBI) 189, 253
PA0661 PA0661 hypothetical protein (NCBI) 338, 368
PA0759 PA0759 hypothetical protein (NCBI) 123, 338
PA0820 PA0820 hypothetical protein (NCBI) 338, 383
PA0873 phhR transcriptional regulator PhhR (NCBI) 33, 338
PA0918 PA0918 cytochrome b561 (NCBI) 26, 189
PA0979 PA0979 hypothetical protein (NCBI) 231, 338
PA1038 PA1038 hypothetical protein (NCBI) 338, 483
PA1039 PA1039 hypothetical protein (NCBI) 3, 338
PA1040 PA1040 hypothetical protein (NCBI) 338, 378
PA1043 PA1043 hypothetical protein (NCBI) 338, 384
PA1201 PA1201 probable transcriptional regulator (NCBI) 53, 338
PA1203 PA1203 hypothetical protein (NCBI) 258, 338
PA1204 PA1204 hypothetical protein (NCBI) 338, 523
PA1243 PA1243 probable sensor/response regulator hybrid (NCBI) 189, 226
PA1686 alkA DNA-3-methyladenine glycosidase II (NCBI) 189, 229
PA1819 PA1819 probable amino acid permease (NCBI) 87, 338
PA1834 PA1834 hypothetical protein (NCBI) 189, 321
PA1890 PA1890 probable glutathione S-transferase (NCBI) 70, 338
PA1929 PA1929 hypothetical protein (NCBI) 189, 295
PA1996 ppiC1 peptidyl-prolyl cis-trans isomerase C1 (NCBI) 41, 338
PA2079 PA2079 probable amino acid permease (NCBI) 189, 197
PA2088 PA2088 hypothetical protein (NCBI) 189, 287
PA2182 PA2182 hypothetical protein (NCBI) 189, 521
PA2196 PA2196 probable transcriptional regulator (NCBI) 189, 291
PA2229 PA2229 hypothetical protein (NCBI) 34, 189
PA2230 PA2230 hypothetical protein (NCBI) 189, 206
PA2246 bkdR transcriptional regulator BkdR (NCBI) 338, 346
PA2306 PA2306 hypothetical protein (NCBI) 257, 338
PA2318 PA2318 hypothetical protein (NCBI) 189, 381
PA2378 PA2378 probable aldehyde dehydrogenase (NCBI) 257, 338
PA2379 PA2379 probable oxidoreductase (NCBI) 257, 338
PA2679 PA2679 hypothetical protein (NCBI) 189, 190
PA2850 ohr organic hydroperoxide resistance protein (NCBI) 189, 255
PA3037 PA3037 hypothetical protein (NCBI) 189, 377
PA3118 leuB 3-isopropylmalate dehydrogenase (NCBI) 338, 462
PA3119 PA3119 hypothetical protein (NCBI) 189, 291
PA3205 PA3205 hypothetical protein (NCBI) 189, 342
PA3211 PA3211 probable permease of ABC transporter (NCBI) 60, 338
PA3212 PA3212 probable ATP-binding component of ABC transporter (NCBI) 81, 338
PA3221 csaA CsaA protein (NCBI) 189, 226
PA3222 PA3222 hypothetical protein (NCBI) 189, 268
PA3475 pheC cyclohexadienyl dehydratase precursor (NCBI) 170, 338
PA3602 PA3602 hypothetical protein (NCBI) 189, 361
PA3719 PA3719 hypothetical protein (NCBI) 189, 224
PA3720 PA3720 hypothetical protein (NCBI) 189, 224
PA3721 PA3721 probable transcriptional regulator (NCBI) 189, 212
PA4308 PA4308 hypothetical protein (NCBI) 338, 462
PA4444 mltB1 membrane-bound lytic transglycosylase (NCBI) 166, 338
PA4539 PA4539 hypothetical protein (NCBI) 189, 313
PA4594 PA4594 probable ATP-binding component of ABC transporter (NCBI) 338, 397
PA4734 PA4734 hypothetical protein (NCBI) 313, 338
PA4955 PA4955 hypothetical protein (NCBI) 338, 457
PA5035 gltD glutamate synthase small chain (NCBI) 62, 189
PA5314 PA5314 hypothetical protein (NCBI) 187, 338
PA5349 PA5349 probable rubredoxin reductase (NCBI) 20, 338
PA5350 rubA2 rubredoxin 2 (NCBI) 212, 338
PA5445 PA5445 probable coenzyme A transferase (NCBI) 138, 189
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 PA0367
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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