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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Filtered green Value Type network_comparison Interaction Map red Gene Rank Network Comparison Type description

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green	Value Type	network_comparison	Interaction Map	red	Rank	Network Comparison Type	description
1.87479	Squared	1.87479	High confidence	0	439	Subtracted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
			Low confidence		797		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
					798		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
					799		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
		187479	High confidence	0.00001	5	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
					6		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
					7		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
			Low confidence		1		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
					2		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
					3		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
2.13609		0.76899		1.3671	806	Subtracted	protein c20orf142 precursor. [swissprot;acc:q8n6m3]
		1.5625		1.3671	150	Divided	protein c20orf142 precursor. [swissprot;acc:q8n6m3]
		2.87214	High confidence	6.13515	75	Divided	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
		3.99906	High confidence	6.13515	422	Subtracted
2.17643		3.14882	Low confidence	6.85319	72	Divided	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]
2.17643		4.67676	Low confidence	6.85319	771	Subtracted
2.18581	Rooted	1.96964	High confidence	4.30525	36	Divided	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
2.18581		2.11944	High confidence	4.30525	267	Subtracted
2.21126		7.72053	Low confidence	17.0721	13	Divided	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]
2.21126		14.8608	Low confidence	17.0721	9	Subtracted
2.38124	Squared	4.60852	High confidence	10.974	50	Divided	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]
2.38124		8.59276		10.974	398	Subtracted
2.40686		1.13667		1.27019	444	Subtracted	alpha crystallin a chain. [swissprot;acc:p02489]
2.40686		1.89488		1.27019	121	Divided	alpha crystallin a chain. [swissprot;acc:p02489]
2.81207		2.81207		0	429	Subtracted	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
2.81207		281207		0.00001	4	Divided	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
2.86829		1.37136		4.23965	441	Subtracted	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
2.86829		1.47811		4.23965	184	Divided
2.91621		5.57131	Low confidence	16.2471	50	Divided	latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302]
2.91621		13.3309		16.2471	746	Subtracted
3.00407	Rooted	3.00407		0	273	Subtracted	jumonji protein. [swissprot;acc:q92833]
3.00407		300407		0.00001	9	Divided	jumonji protein. [swissprot;acc:q92833]
3.18113		2.09307		6.65832	21	Divided	dna helicase homolog (fragment). [sptrembl;acc:q9y645]
3.18113		3.47719		6.65832	236	Subtracted	dna helicase homolog (fragment). [sptrembl;acc:q9y645]
3.28686	Squared	0.46043		2.82643	816	Subtracted	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
3.28686	Squared	1.1629		2.82643	317	Divided
3.38392	Rooted	0.73817	High confidence	2.64575	399	Subtracted	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]
		0.73817	Low confidence		641	Subtracted
		1.279	High confidence		109	Divided
		1.279	Low confidence		105	Divided
3.43037	Squared	2.58092	High confidence	0.849445	432	Subtracted	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]
3.43037	Squared	4.03837		0.849445	57	Divided
3.64637	Rooted	2.63946		9.62443	28	Divided	syntaxin 10 (syn10). [swissprot;acc:o60499]
3.64637		5.97806		9.62443	72	Subtracted	syntaxin 10 (syn10). [swissprot;acc:o60499]
3.80565		3.62106		13.7805	25	Divided	60s ribosomal protein l37a. [swissprot;acc:p12751]
		3.62106			26	Divided	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]
		9.97485			27	Subtracted	60s ribosomal protein l37a. [swissprot;acc:p12751]
		9.97485			28	Subtracted	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]
3.83288	Squared	4.04283		15.4957	56	Divided	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]
3.83288	Squared	11.6628		15.4957	393	Subtracted

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

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