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

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Showing element 1 to 50 of 29840 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 0

Rank	description	Network Comparison Type	red	green	network_comparison
1	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	85	6410	6325
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364	0.00001	36400000
2	cab2. [refseq;acc:nm_033419]		0.00001	174	17400000
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	85	6410	6325
3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		23818.1	19621.3	4196.8
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	0.00001	109	10900000
4	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			89	8900000
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	18704	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]	Divided	0.00001	89	8900000
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	13174.7	15605.1	2430.4
7	sedlin. [swissprot;acc:o14582]	Divided	0.00001	43	4300000
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	13174.7	15605.1	2430.4
8	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]		5106.93	7500.75	2393.82
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Divided	0.00001	43	4300000
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Subtracted	12478	14756	2278
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Divided	85	6410	75.4118
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Subtracted	7830.62	6193.07	1637.55
11	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		5734.28	7252.02	1517.74
	serpin b12. [swissprot;acc:q96p63]	Divided	199.549	5.56738	35.8425
12	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	5629.62	7099.51	1469.89
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	199.249	5.71669	34.8539
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		1363	47	29
		Subtracted			1316
14	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]		10817.1	12125.1	1308
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	130.512	6.50325	20.0687
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]		10	156	15.6
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Subtracted	7981.68	6685.11	1296.57
16	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		8852.4	7572.88	1279.52
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Divided	1	15	15
17	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted	11223	12473	1250
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	859	58	14.8103
18	60s ribosomal protein l37a. [swissprot;acc:p12751]		305.45	26.1599	11.6763
	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Subtracted	15411.3	14167	1244.3
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Divided	305.45	26.1599	11.6763
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Subtracted	1593	2804	1211
20	ero1-like. [refseq;acc:nm_014584]	Divided	82	0.00001	8200000
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Subtracted	8763	7608	1155
21	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]		6804.88	5690.63	1114.25
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	118.878	17.6611	6.73106
22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60	0.00001	6000000
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Subtracted	31122	30022.4	1099.6
23	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		6596.23	5540.2	1056.03
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Divided	0.00001	59	5900000
24	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	3233.86	2208.1	1025.76
	ptd016 protein. [refseq;acc:nm_016125]	Divided	30	158	5.26667
25	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Subtracted	459.5	1377	917.5
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided	148	773	5.22297

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.