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 [...,...].
% Affected Genes Average Regulation (ratio) 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

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\% Affected Genes\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Average Regulation (ratio)\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Would Be Affected (#genes)\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
Class Size (#genes)\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
Class\vspace{3pt}}\\
\hline
\hline
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142\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
protein amino acid dephosphorylation\vspace{3pt}}\\\hline
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muscle development\vspace{3pt}}\\\hline
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158\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
dephosphorylation\vspace{3pt}}\\\hline
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107\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
embryonic morphogenesis\vspace{3pt}}\\\hline
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226\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
response to cold\vspace{3pt}}\\\hline
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142\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
mitosis\vspace{3pt}}\\\hline
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217\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
homoiothermy\vspace{3pt}}\\\hline
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response to temperature stimulus\vspace{3pt}}\\\hline
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226\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
thermoregulation\vspace{3pt}}\\\hline
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regulation of progression through cell cycle\vspace{3pt}}\\\cline{1-1}\cline{4-5}
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539\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of cell cycle\vspace{3pt}}\\\hline
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regulation of growth\vspace{3pt}}\\\hline
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164\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
transmembrane receptor protein tyrosine kinase signaling pathway\vspace{3pt}}\\\hline
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230\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
enzyme linked receptor protein signaling pathway\vspace{3pt}}\\\hline
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RNA splicing\vspace{3pt}}\\\hline
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cell cycle process\vspace{3pt}}\\\hline
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organ morphogenesis\vspace{3pt}}\\\hline
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cell cycle phase\vspace{3pt}}\\\hline
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regulation of cell differentiation\vspace{3pt}}\\\hline
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378\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
alcohol metabolic process\vspace{3pt}}\\\hline
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phosphate metabolic process\vspace{3pt}}\\\cline{5-5}
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phosphorus metabolic process\vspace{3pt}}\\\hline
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1721\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
protein modification process\vspace{3pt}}\\\hline
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cell division\vspace{3pt}}\\\hline
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response to stress\vspace{3pt}}\\\hline
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positive regulation of transcription\vspace{3pt}}\\\hline
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499\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of transcription from RNA polymerase II promoter\vspace{3pt}}\\\hline
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1442\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
post-translational protein modification\vspace{3pt}}\\\hline
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195\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
chromatin modification\vspace{3pt}}\\\hline
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2.470501118236118\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
52\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
1780\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
biopolymer modification\vspace{3pt}}\\\hline
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2.9289\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.6086528982434953\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
9\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
318\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
inflammatory response\vspace{3pt}}\\\hline
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2.4850547462701797\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
10\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
358\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
response to wounding\vspace{3pt}}\\\hline
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6\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
206\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
nucleocytoplasmic transport\vspace{3pt}}\\\hline
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2.8939\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.3975469536251492\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
10\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
347\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process\vspace{3pt}}\\\hline
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12\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
416\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
response to abiotic stimulus\vspace{3pt}}\\\hline
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2.5862315134568648\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
13\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
443\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
ubiquitin cycle\vspace{3pt}}\\\hline
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2.1418599311043236\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
19\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
686\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
anatomical structure morphogenesis\vspace{3pt}}\\\hline
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211\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
visual perception\vspace{3pt}}\\\cline{1-1}\cline{4-5}
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212\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
sensory perception of light stimulus\vspace{3pt}}\\\cline{1-2}\cline{4-5}
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231\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
microtubule-based process\vspace{3pt}}\\\hline
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33\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
1217\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
intracellular signaling cascade\vspace{3pt}}\\\hline
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1.6556044340133667\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
6\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
229\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
anion transport\vspace{3pt}}\\\hline
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2.6362\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.630213709672292\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
42\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
1588\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
transcription\vspace{3pt}}\\\hline
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2.6247\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.28793443441391\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
11\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
429\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
positive regulation of cellular metabolic process\vspace{3pt}}\\\hline
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2.6245\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.3178554457061145\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
69\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
2628\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of transcription\vspace{3pt}}\\\hline
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2.6235\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.3607054107329426\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
20\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
768\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
protein transport\vspace{3pt}}\\\hline
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2.6201\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.6820639967918396\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
19\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
735\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
immune response\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2.6103\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.1811264465595115\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
33\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
1273\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
anatomical structure development\vspace{3pt}}\\\hline
nd{longtable}

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/