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	red	Network Comparison Type	green	network_comparison

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Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Filtered  : 0

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