Organism : Pseudomonas aeruginosa | Module List :
PA5550 glmR

GlmR transcriptional regulator (NCBI)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism 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 PA5550
(Mouseover regulator name to see its description)

PA5550 is regulated by 45 influences and regulates 82 modules.
Regulators for PA5550 glmR (45)
Regulator Module Operator
PA0179 40 tf
PA0376 40 tf
PA0784 40 tf
PA0815 40 tf
PA0890 40 tf
PA0961 40 tf
PA1067 40 tf
PA1998 40 tf
PA2016 40 tf
PA2556 40 tf
PA3002 40 tf
PA3126 40 tf
PA3604 40 tf
PA3778 40 tf
PA4052 40 tf
PA4853 40 tf
PA4890 40 tf
PA5356 40 tf
PA5389 40 tf
PA5403 40 tf
PA5431 40 tf
PA5511 40 tf
PA5550 40 tf
PA0120 520 tf
PA0179 520 tf
PA0436 520 tf
PA0961 520 tf
PA1141 520 tf
PA1898 520 tf
PA2047 520 tf
PA2622 520 tf
PA2737 520 tf
PA2921 520 tf
PA3002 520 tf
PA3477 520 tf
PA3583 520 tf
PA3604 520 tf
PA3778 520 tf
PA4052 520 tf
PA4074 520 tf
PA4451 520 tf
PA4853 520 tf
PA4890 520 tf
PA5324 520 tf
PA5550 520 tf
Regulated by PA5550 (82)
Module Residual Genes
1 0.52 19
14 0.55 17
17 0.40 16
28 0.53 23
40 0.52 21
45 0.44 18
55 0.48 19
64 0.42 12
65 0.50 26
66 0.43 19
78 0.54 18
83 0.45 21
84 0.50 22
86 0.59 20
99 0.55 19
102 0.36 11
103 0.52 18
131 0.54 18
133 0.44 13
135 0.49 21
141 0.47 14
153 0.47 17
162 0.53 23
163 0.56 25
170 0.59 33
174 0.48 16
181 0.52 25
185 0.54 19
195 0.57 21
204 0.47 18
207 0.45 18
209 0.52 22
214 0.50 19
230 0.43 16
247 0.49 26
258 0.53 17
260 0.44 12
262 0.40 11
264 0.51 15
269 0.45 16
270 0.46 19
272 0.41 13
277 0.45 19
294 0.50 21
308 0.41 12
312 0.48 15
314 0.44 14
322 0.45 19
332 0.52 19
341 0.58 19
349 0.45 17
353 0.50 21
360 0.41 13
361 0.53 23
374 0.55 31
382 0.48 20
389 0.60 24
396 0.49 19
397 0.51 28
404 0.42 12
413 0.37 9
416 0.42 15
421 0.46 17
422 0.52 21
427 0.41 13
431 0.44 19
442 0.51 21
451 0.51 15
452 0.59 23
475 0.52 25
483 0.49 32
487 0.49 23
492 0.39 11
493 0.55 18
495 0.33 12
499 0.55 24
510 0.37 10
520 0.45 17
528 0.51 22
548 0.34 10
552 0.48 13
555 0.36 11
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2912 1.90e+03 GcCGCcgcccGGCGG
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2913 9.70e+04 GCcGcCGctGTCcTT
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3854 1.50e-03 tA.aat.gcgccctTtt
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3855 1.60e+03 AaaaGATTTT
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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 PA5550

PA5550 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism 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 PA5550

PA5550 has total of 35 gene neighbors in modules 40, 520
Gene neighbors (35)
Gene Common Name Description Module membership
PA0380 PA0380 sulfur carrier protein ThiS (NCBI) 111, 520
PA0386 PA0386 coproporphyrinogen III oxidase (NCBI) 40, 207
PA0389 PA0389 hypothetical protein (NCBI) 40, 207
PA0438 codB cytosine permease (NCBI) 40, 377
PA0592 ksgA dimethyladenosine transferase (NCBI) 308, 520
PA0774 PA0774 hypothetical protein (NCBI) 40, 377
PA0860 PA0860 probable ATP-binding/permease fusion ABC transporter (NCBI) 40, 65
PA0944 purN phosphoribosylglycinamide formyltransferase (NCBI) 272, 520
PA1045 PA1045 hypothetical protein (NCBI) 442, 520
PA1271 PA1271 probable tonB-dependent receptor (NCBI) 83, 520
PA1591 PA1591 hypothetical protein (NCBI) 40, 335
PA1687 speE spermidine synthase (NCBI) 314, 520
PA1971 braZ branched chain amino acid transporter BraZ (NCBI) 40, 65
PA2038 PA2038 hypothetical protein (NCBI) 40, 247
PA2042 PA2042 probable transporter (membrane subunit) (NCBI) 40, 398
PA3246 rluA pseudouridine synthase RluA (NCBI) 40, 520
PA3263 rdgC recombination associated protein (NCBI) 442, 520
PA3824 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI) 404, 520
PA3967 PA3967 hypothetical protein (NCBI) 422, 520
PA4050 pgpA phosphatidylglycerophosphatase A (NCBI) 40, 520
PA4438 PA4438 hypothetical protein (NCBI) 39, 520
PA4562 PA4562 hypothetical protein (NCBI) 40, 377
PA4616 PA4616 probable c4-dicarboxylate-binding protein (NCBI) 40, 218
PA4627 PA4627 hypothetical protein (NCBI) 332, 520
PA4628 lysP lysine-specific permease (NCBI) 40, 207
PA4684 PA4684 hypothetical protein (NCBI) 86, 520
PA4961 PA4961 hypothetical protein (NCBI) 40, 100
PA5121 PA5121 hypothetical protein (NCBI) 40, 375
PA5156 PA5156 hypothetical protein (NCBI) 40, 65
PA5193 hslO Hsp33-like chaperonin (NCBI) 422, 520
PA5201 PA5201 hypothetical protein (NCBI) 90, 520
PA5404 PA5404 hypothetical protein (NCBI) 40, 65
PA5478 PA5478 hypothetical protein (NCBI) 40, 377
PA5518 PA5518 probable potassium efflux transporter (NCBI) 40, 375
PA5550 glmR GlmR transcriptional regulator (NCBI) 40, 520
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 PA5550
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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