Organism : Pseudomonas aeruginosa | Module List :
PA0456

probable cold-shock protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0456
(Mouseover regulator name to see its description)

PA0456 is regulated by 27 influences and regulates 33 modules.
Regulators for PA0456 (27)
Regulator Module Operator
PA0456 327 tf
PA0610 327 tf
PA0652 327 tf
PA1099 327 tf
PA1159 327 tf
PA1544 327 tf
PA2849 327 tf
PA2885 327 tf
PA3965 327 tf
PA4315 327 tf
PA4745 327 tf
PA4755 327 tf
PA5253 327 tf
PA5374 327 tf
PA0376 210 tf
PA0456 210 tf
PA1159 210 tf
PA2931 210 tf
PA2957 210 tf
PA3266 210 tf
PA3815 210 tf
PA4275 210 tf
PA4315 210 tf
PA4451 210 tf
PA4745 210 tf
PA4764 210 tf
PA4853 210 tf
Regulated by PA0456 (33)
Module Residual Genes
6 0.53 23
13 0.42 12
41 0.56 20
59 0.54 21
69 0.41 13
84 0.50 22
127 0.56 28
182 0.45 14
210 0.38 13
217 0.32 11
219 0.27 12
224 0.61 26
228 0.51 17
232 0.46 13
243 0.57 28
261 0.53 16
271 0.52 17
315 0.59 21
327 0.53 19
352 0.43 9
354 0.47 15
361 0.53 23
398 0.48 18
402 0.51 20
419 0.32 11
424 0.43 13
454 0.34 11
490 0.52 19
506 0.32 9
531 0.31 11
539 0.28 12
541 0.55 23
548 0.34 10
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3248 1.50e-01 acctCctTgCAAcTgaGTA
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3249 1.80e+03 GGAtATta
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3480 1.40e-03 tA.aattggt.aTtATTt
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3481 3.30e-01 TttttgtCGgGctTTttttcCC
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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 PA0456

PA0456 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Cold shock proteins cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA0456

PA0456 has total of 31 gene neighbors in modules 210, 327
Gene neighbors (31)
Gene Common Name Description Module membership
PA0432 sahH S-adenosyl-L-homocysteine hydrolase (NCBI) 19, 327
PA0456 PA0456 probable cold-shock protein (NCBI) 210, 327
PA0579 rpsU 30S ribosomal protein S21 (NCBI) 210, 454
PA1544 anr transcriptional regulator Anr (NCBI) 327, 524
PA2741 rplT 50S ribosomal protein L20 (NCBI) 210, 217
PA2742 rpmI 50S ribosomal protein L35 (NCBI) 182, 210
PA2743 infC translation initiation factor IF-3 (NCBI) 182, 210
PA2966 acpP acyl carrier protein (NCBI) 1, 210
PA2970 rpmF 50S ribosomal protein L32 (NCBI) 210, 217
PA3266 capB cold acclimation protein B (NCBI) 210, 251
PA3531 bfrB bacterioferritin (NCBI) 296, 327
PA3533 PA3533 hypothetical protein (NCBI) 6, 327
PA3940 PA3940 probable DNA binding protein (NCBI) 6, 327
PA4264 rpsJ 30S ribosomal protein S10 (NCBI) 210, 539
PA4395 PA4395 hypothetical protein (NCBI) 6, 327
PA4567 rpmA 50S ribosomal protein L27 (NCBI) 210, 352
PA4568 rplU 50S ribosomal protein L21 (NCBI) 210, 419
PA4944 hfq RNA-binding protein Hfq (NCBI) 182, 327
PA4971 aspP adenosine diphosphate sugar pyrophosphatase (NCBI) 327, 368
PA5068 tatA twin argininte translocase protein A (NCBI) 182, 327
PA5240 trxA thioredoxin (NCBI) 210, 251
PA5300 cycB cytochrome c5 (NCBI) 281, 327
PA5303 PA5303 hypothetical protein (NCBI) 238, 327
PA5304 dadA D-amino acid dehydrogenase small subunit (NCBI) 238, 327
PA5315 rpmG 50S ribosomal protein L33 (NCBI) 210, 454
PA5373 betB betaine aldehyde dehydrogenase (NCBI) 327, 524
PA5374 betI transcriptional regulator BetI (NCBI) 327, 524
PA5489 dsbA thiol:disulfide interchange protein DsbA (NCBI) 6, 327
PA5490 cc4 cytochrome c4 precursor (NCBI) 165, 327
PA5505 PA5505 probable TonB-dependent receptor (NCBI) 327, 543
PA5528 PA5528 hypothetical protein (NCBI) 8, 327
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 PA0456
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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