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	Network Comparison Type	red	network_comparison	green

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Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Filtered  : 0

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