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

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Showing element 1 to 50 of 29840 in total

Filtered  : 0
Interaction Map  : High confidence

Rank	Value Type	description	Network Comparison Type	green	red	network_comparison
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	6410	85	6325
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	364	36400000
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		15915	4294	3.70633
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	21883	8906	12977
	Squared	cab2. [refseq;acc:nm_033419]	Divided	7.16592	0.00001	716592
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	160184	232467	72283
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		60.0707	9.20014	50.8706
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	19.0788	1907880
2	Measured	cab2. [refseq;acc:nm_033419]		174	0.00001	17400000
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	6410	85	6325
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		15915	4294	11621
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	14977	5865	2.55362
	Squared	histone h4. [swissprot;acc:p02304]	Subtracted	345123	273623	71500
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0.00001	5.61325	561325
	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	60.0707	9.20014	50.8706
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0.00001	12.4097	1240970
3	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	19621.3	23818.1	4196.8
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	109	0.00001	10900000
	Ranked	cab2. [refseq;acc:nm_033419]	Subtracted	10950	21866	10916
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Divided	11083.9	4475.84	2.47638
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Subtracted	170628	135280	35348
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0.00001	5.61325	561325
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	6.85565	36.9188	30.0631
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0.00001	12.4097	1240970
4	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	0.00001	8900000
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	21730	18704	3026
	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	21883	8906	2.45711
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Subtracted	21888	11525	10363
	Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	2.81207	0.00001	281207
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	105900	75446.7	30453.3
	Rooted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		7.61577	29.3087	21.6929
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	10.4403	0.00001	1044030
5	Measured	histone h4. [swissprot;acc:p02304]	Subtracted	24446.3	21773.1	2673.2
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	89	0.00001	8900000
	Ranked	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Subtracted	21888	11525	10363
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Divided	11965.7	5510.5	2.17144
	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.87479	0.00001	187479
		zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	105900	75446.7	30453.3
	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	9.43398	0.00001	943398
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	0	19.0788	19.0788
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	89	0.00001	8900000
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	15605.1	13174.7	2430.4
	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	5865	9112
		ubiquitin protein ligase. [refseq;acc:nm_130466]	Divided	15339.2	7523	2.03897
	Squared	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Subtracted	102814	73080.8	29733.2
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	1.87479	0.00001	187479
	Rooted			9.43398		943398
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Subtracted	27.8029	12.1655	15.6374
7	Measured	sedlin. [swissprot;acc:o14582]	Divided	43	0.00001	4300000
		zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	15605.1	13174.7	2430.4

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.