Scientific

MK5 Microarray Data


Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis
Session lost

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20) Resetting the view coordinate localhost/Mk5/go_classes/


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Average Regulation (ratio) % Affected Genes Would Be Affected (#genes) Class Size (#genes) Class Class affected Microarray Measured (#genes) Accession
Results: HTML CSV LaTeX Showing element 1 to 50 of 173 in total
Class  : biological process
Average Regulation (ratio)
% Affected Genes
Would Be Affected (#genes)
Class Size (#genes)
Class
3.175950493131365 2.5000 10 416 establishment and/or maintenance of chromatin architecture
2.4561 422 DNA packaging
2.0349 496 chromosome organization and biogenesis (sensu Eukaryota)
3.0782742261886598 2.2026 15 680 defense response
3.0316067695617677 2.7174 6 231 microtubule-based process
2.9956377029418944 2.9412 195 chromatin modification
2.941256210207939 2.1858 11 519 chromosome organization and biogenesis
2.8815125972032547 2.4922 9 379 apoptosis
2.4845 381 programmed cell death
2.844642996788025 2.9070 6 206 nucleocytoplasmic transport
2.8162122435039945 2.4658 11 430 cell death
death
2.7829527854919434 2.8249 6 211 visual perception
2.8090 212 sensory perception of light stimulus
2.7678764888218472 2.6820 33 1217 intracellular signaling cascade
2.745920252799988 1.1390 6 544 carbohydrate metabolic process
2.7119380235671997 1.8182 10 531 cytoskeleton organization and biogenesis
2.6960288683573403 2.4064 11 442 small GTPase mediated signal transduction
2.6894871592521667 5.7692 7 117 muscle development
2.6829177481787547 3.9773 8 192 regulation of growth
2.6820639967918396 2.6201 19 735 immune response
2.644248050451279 2.1413 26 1204 organelle organization and biogenesis
2.6417386531829834 2.5890 18 711 phosphorylation
2.6329536702897816 5.0000 11 226 response to cold
4.4554 249 response to temperature stimulus
2.630213709672292 2.6362 42 1588 transcription
2.6115847550905666 2.2184 20 879 immune system process
2.6086528982434953 2.9289 9 318 inflammatory response
2.5862315134568648 2.8646 13 443 ubiquitin cycle
2.5815784772237143 2.5554 17 675 protein amino acid phosphorylation
2.539123611790793 2.5045 16 644 organ development
2.5307046931523542 2.3508 70 2985 response to stimulus
2.530326783657074 2.8736 12 416 response to abiotic stimulus
2.5267262917298536 1.9118 17 884 DNA metabolic process
2.5005394551489086 1.8711 21 1118 cellular developmental process
2.4850547462701797 2.9197 10 358 response to wounding
2.4829982866843543 3.0968 28 890 phosphate metabolic process
phosphorus metabolic process
2.470501118236118 3.0405 52 1721 protein modification process
2.9393 1780 biopolymer modification
2.46775693159837 2.9680 15 499 regulation of transcription from RNA polymerase II promoter
2.453812837600708 1.9231 11 552 translation
2.4479837675352356 2.9529 43 1442 post-translational protein modification
2.4382004340489707 2.2514 16 732 sensory perception
2.2181 741 neurological process
2.4346015453338623 1.8051 6 325 negative regulation of transcription
2.4306948675828823 2.1879 67 3075 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
2.43051519464044 2.0821 42 2008 cellular component organization and biogenesis
2.416864479581515 2.3483 34 1453 G-protein coupled receptor protein signaling pathway
2.4153901100158692 2.0161 6 292 potassium ion transport

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.

- http://analysis.yellowcouch.org/