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	Interaction Map	green	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	Interaction Map	green	red	Network Comparison Type	network_comparison
1	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	6410	85	Subtracted	6325
		Low confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	0.00001	364	Divided	36400000
		Low confidence
2	cab2. [refseq;acc:nm_033419]	High confidence	174	0.00001		17400000
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	89			8900000
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	6410	85	Subtracted	6325
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence	19621.3	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]	High confidence	19621.3	23818.1	Subtracted	4196.8
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Low confidence	7500.75	5106.93		2393.82
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	109	0.00001	Divided	10900000
4	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Low confidence	4356	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]	Low confidence	17.5166			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]	High confidence	89	0.00001	Divided	8900000
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	0.00001	13		1300000
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	High confidence	15605.1	13174.7	Subtracted	2430.4
		Low confidence	8836.85	7592.37		1244.48
7	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		5898.71	4660.09		1238.62
	sedlin. [swissprot;acc:o14582]	High confidence	43	0.00001	Divided	4300000
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	0.00001	2.31962		231962
	zinc finger protein 277. [swissprot;acc:q9nrm2]	High confidence	15605.1	13174.7	Subtracted	2430.4
8	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Low confidence	6410	85	Divided	75.4118
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	High confidence	7500.75	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]	Low confidence	8770.72	7537.89	Subtracted	1232.83
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	High confidence	14756	12478		2278
		Low confidence	11468.3	10255.7		1212.6
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	6410	85	Divided	75.4118
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence	10.6048	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]	High confidence	6410	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]	Low confidence	5.56738	199.549	Divided	35.8425
11	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	High confidence	7252.02	5734.28	Subtracted	1517.74
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Low confidence	5341.81	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]	High confidence	5.56738	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]	Low confidence	58	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]	High confidence	47	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.