Scientific

MK5 Microarray Data


Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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)


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