Organism : Pseudomonas aeruginosa | Module List :
PA3428

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3428
(Mouseover regulator name to see its description)

PA3428 is regulated by 35 influences and regulates 0 modules.
Regulators for PA3428 (35)
Regulator Module Operator
PA1290 74 tf
PA1347 74 tf
PA1351 74 tf
PA1399 74 tf
PA1504 74 tf
PA1864 74 tf
PA3381 74 tf
PA3420 74 tf
PA3594 74 tf
PA3596 74 tf
PA4147 74 tf
PA4238 74 tf
PA4341 74 tf
PA4769 74 tf
PA5116 74 tf
PA5337 74 tf
PA0701 446 tf
PA1347 446 tf
PA2050 446 tf
PA2258 446 tf
PA2276 446 tf
PA2354 446 tf
PA2376 446 tf
PA2447 446 tf
PA2519 446 tf
PA2547 446 tf
PA2785 446 tf
PA2838 446 tf
PA3420 446 tf
PA3594 446 tf
PA3596 446 tf
PA4169 446 tf
PA4341 446 tf
PA5032 446 tf
PA5293 446 tf

Warning: PA3428 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
2980 2.90e+01 ATAACGA
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2981 5.10e+03 GtAaGaCCGGCGAca
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3712 3.30e+02 tGTTTCC
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3713 1.70e+03 TaATCgAACcGAAcC
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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 PA3428

Warning: No Functional annotations were found!

Module neighborhood information for PA3428

PA3428 has total of 48 gene neighbors in modules 74, 446
Gene neighbors (48)
Gene Common Name Description Module membership
PA0146 PA0146 hypothetical protein (NCBI) 74, 333
PA0147 PA0147 probable oxidoreductase (NCBI) 74, 87
PA0240 PA0240 probable porin (NCBI) 394, 446
PA0451 PA0451 hypothetical protein (NCBI) 74, 475
PA0452 PA0452 probable stomatin-like protein (NCBI) 74, 546
PA0507 PA0507 probable acyl-CoA dehydrogenase (NCBI) 74, 373
PA0532 PA0532 hypothetical protein (NCBI) 74, 292
PA0585 PA0585 hypothetical protein (NCBI) 74, 136
PA1219 PA1219 hypothetical protein (NCBI) 74, 401
PA1251 PA1251 probable chemotaxis transducer (NCBI) 394, 446
PA1743 PA1743 hypothetical protein (NCBI) 108, 446
PA1864 PA1864 probable transcriptional regulator (NCBI) 74, 546
PA2257 pvcD pyoverdine biosynthesis protein PvcD (NCBI) 199, 446
PA2286 PA2286 hypothetical protein (NCBI) 199, 446
PA2346 PA2346 hypothetical protein (NCBI) 304, 446
PA2347 PA2347 hypothetical protein (NCBI) 289, 446
PA2350 PA2350 probable ATP-binding component of ABC transporter (NCBI) 235, 446
PA2351 PA2351 probable permease of ABC transporter (NCBI) 235, 446
PA2357 msuE NADH-dependent FMN reductase MsuE (NCBI) 156, 446
PA2437 PA2437 hypothetical protein (NCBI) 320, 446
PA2438 PA2438 hypothetical protein (NCBI) 446, 519
PA2439 PA2439 hypothetical protein (NCBI) 199, 446
PA2519 xylS transcriptional regulator XylS (NCBI) 172, 446
PA2520 czcA Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux transporter CzcA (NCBI) 24, 446
PA2521 czcB Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux membrane fusion protein CzcB precursor (NCBI) 175, 446
PA2522 czcC outer membrane protein precursor CzcC (NCBI) 418, 446
PA2531 PA2531 putative aminotransferase (NCBI) 74, 190
PA2662 PA2662 hypothetical protein (NCBI) 74, 110
PA2663 PA2663 hypothetical protein (NCBI) 74, 110
PA2711 PA2711 probable periplasmic spermidine/putrescine-binding protein (NCBI) 74, 294
PA3032 snr1 cytochrome c Snr1 (NCBI) 74, 432
PA3396 nosL NosL protein (NCBI) 74, 497
PA3421 PA3421 hypothetical protein (NCBI) 74, 545
PA3428 PA3428 hypothetical protein (NCBI) 74, 446
PA3429 PA3429 probable epoxide hydrolase (NCBI) 74, 211
PA3430 PA3430 hypothetical protein (NCBI) 74, 211
PA3946 PA3946 probable two-component sensor (NCBI) 201, 446
PA4096 PA4096 probable major facilitator superfamily (MFS) transporter (NCBI) 446, 545
PA4097 PA4097 probable alcohol dehydrogenase (Zn-dependent) (NCBI) 446, 545
PA4509 PA4509 hypothetical protein (NCBI) 53, 74
PA4591 PA4591 hypothetical protein (NCBI) 74, 197
PA4844 PA4844 probable chemotaxis transducer (NCBI) 68, 74
PA4908 PA4908 ornithine cyclodeaminase (NCBI) 74, 97
PA4910 PA4910 probable ATP-binding component of ABC transporter (NCBI) 74, 470
PA4911 PA4911 probable permease of ABC branched-chain amino acid transporter (NCBI) 74, 470
PA5082 PA5082 probable binding protein component of ABC transporter (NCBI) 62, 74
PA5083 PA5083 hypothetical protein (NCBI) 74, 343
PA5084 PA5084 probable oxidoreductase (NCBI) 74, 343
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 PA3428
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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