MK5 Microarray Data

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

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Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Filtered  : 0

Rank	description	green	Interaction Map	red	Network Comparison Type	network_comparison
1	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	High confidence	85	Subtracted	6325
			Low confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	364	Divided	36400000
			Low confidence
2	cab2. [refseq;acc:nm_033419]	174	High confidence	0.00001		17400000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Low confidence			8900000
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	85	Subtracted	6325
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Low confidence	23818.1		4196.8
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		0.00001	Divided	8900000
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	High confidence	23818.1	Subtracted	4196.8
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	Low confidence	5106.93		2393.82
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	High confidence	0.00001	Divided	10900000
4	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	Low confidence	2082	Subtracted	2274
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89		0.00001	Divided	8900000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		High confidence
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730		18704	Subtracted	3026
5	histone h4. [swissprot;acc:p02304]	24446.3		21773.1		2673.2
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		0.00001	Divided	8900000
	jumonji protein. [swissprot;acc:q92833]	17.5166	Low confidence			1751660
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	2740.13		485.286	Subtracted	2254.84
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	High confidence	0.00001	Divided	8900000
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	Low confidence	13		1300000
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	8836.85		7592.37	Subtracted	1244.48
		15605.1	High confidence	13174.7		2430.4
7	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	5898.71	Low confidence	4660.09		1238.62
	sedlin. [swissprot;acc:o14582]	43	High confidence	0.00001	Divided	4300000
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0.00001	Low confidence	2.31962		231962
	zinc finger protein 277. [swissprot;acc:q9nrm2]	15605.1	High confidence	13174.7	Subtracted	2430.4
8	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	Low confidence	85	Divided	75.4118
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	High confidence	5106.93	Subtracted	2393.82
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43		0.00001	Divided	4300000
	zinc finger protein 277. [swissprot;acc:q9nrm2]	8770.72	Low confidence	7537.89	Subtracted	1232.83
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	11468.3		10255.7		1212.6
		14756	High confidence	12478		2278
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410		85	Divided	75.4118
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	10.6048	Low confidence	383.762		36.1876
10	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2804		1593	Subtracted	1211
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	85	Divided	75.4118
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	6193.07		7830.62	Subtracted	1637.55
	serpin b12. [swissprot;acc:q96p63]	5.56738	Low confidence	199.549	Divided	35.8425
11	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	7252.02	High confidence	5734.28	Subtracted	1517.74
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	5341.81	Low confidence	4230.36		1111.45
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669		199.249	Divided	34.8539
	serpin b12. [swissprot;acc:q96p63]	5.56738	High confidence	199.549		35.8425
12	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	7099.51		5629.62	Subtracted	1469.89
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669		199.249	Divided	34.8539
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	Low confidence	859		14.8103
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	30022.4		31122	Subtracted	1099.6
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	High confidence	1363	Divided	29
					Subtracted	1316

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.