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 Microarray Measured (#genes) affected Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 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
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biopolymer metabolic process\vspace{3pt}}\\\hline
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regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process\vspace{3pt}}\\\hline
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phosphorylation\vspace{3pt}}\\\hline
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protein amino acid phosphorylation\vspace{3pt}}\\\hline
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regulation of transcription, DNA-dependent\vspace{3pt}}\\\hline
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cellular protein metabolic process\vspace{3pt}}\\\hline
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nervous system development\vspace{3pt}}\\\hline
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metabolic process\vspace{3pt}}\\\hline
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13\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
514\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
cell-cell signaling\vspace{3pt}}\\\hline
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cell proliferation\vspace{3pt}}\\\hline
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534\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
intracellular protein transport\vspace{3pt}}\\\hline
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organ development\vspace{3pt}}\\\hline
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416\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
establishment and/or maintenance of chromatin architecture\vspace{3pt}}\\\hline
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cellular macromolecule metabolic process\vspace{3pt}}\\\hline
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establishment of protein localization\vspace{3pt}}\\\hline
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death\vspace{3pt}}\\\hline
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422\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
DNA packaging\vspace{3pt}}\\\hline
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regulation of protein kinase activity\vspace{3pt}}\\\hline
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15431\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
biological\_process\vspace{3pt}}\\\hline
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primary metabolic process\vspace{3pt}}\\\hline
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466\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
system development\vspace{3pt}}\\\hline
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25\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
1036\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
positive regulation of cellular process\vspace{3pt}}\\\hline
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66\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
2739\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
developmental process\vspace{3pt}}\\\hline
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130\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
5408\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
macromolecule metabolic process\vspace{3pt}}\\\hline
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442\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
small GTPase mediated signal transduction\vspace{3pt}}\\\hline
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3018\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of metabolic process\vspace{3pt}}\\\hline
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4348\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of cellular process\vspace{3pt}}\\\hline
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6\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
243\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of kinase activity\vspace{3pt}}\\\hline
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16\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
660\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of biological quality\vspace{3pt}}\\\hline
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6\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
250\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
positive regulation of apoptosis\vspace{3pt}}\\\hline
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establishment of localization\vspace{3pt}}\\\cline{1-2}\cline{4-5}
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2985\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
response to stimulus\vspace{3pt}}\\\hline
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1453\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
G-protein coupled receptor protein signaling pathway\vspace{3pt}}\\\hline
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mRNA processing\vspace{3pt}}\\\cline{2-2}\cline{4-5}
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252\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
positive regulation of programmed cell death\vspace{3pt}}\\\hline
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68\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
2906\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
transport\vspace{3pt}}\\\hline
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2.089855896725374\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
110\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
4730\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
regulation of biological process\vspace{3pt}}\\\hline
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88\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
3816\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
signal transduction\vspace{3pt}}\\\hline
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2.3114\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2.312502180275164\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
96\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
4136\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
cell communication\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/