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	Interaction Map	Filtered	Rank	Gene	green	description	Network Comparison Type	red	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	green	description	Network Comparison Type	red	network_comparison
1	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364	36400000
	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	85	6325
2	174	cab2. [refseq;acc:nm_033419]	Divided	0.00001	17400000
	6410	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	85	6325
3	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	0.00001	10900000
	19621.3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	23818.1	4196.8
4	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	0.00001	8900000
	21730	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	18704	3026
5	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	0.00001	8900000
	24446.3	histone h4. [swissprot;acc:p02304]	Subtracted	21773.1	2673.2
6	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	0.00001	8900000
	15605.1	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	13174.7	2430.4
7	43	sedlin. [swissprot;acc:o14582]	Divided	0.00001	4300000
	15605.1	zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	13174.7	2430.4
8	43	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Divided	0.00001	4300000
	7500.75	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	5106.93	2393.82
9	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Divided	85	75.4118
	14756	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Subtracted	12478	2278
10	6193.07	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]		7830.62	1637.55
	6410	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Divided	85	75.4118
11	5.56738	serpin b12. [swissprot;acc:q96p63]		199.549	35.8425
	7252.02	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	5734.28	1517.74
12	5.71669	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	199.249	34.8539
	7099.51	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	5629.62	1469.89
13	47	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Divided	1363	29
			Subtracted		1316
14	6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	130.512	20.0687
	12125.1	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Subtracted	10817.1	1308
15	156	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]	Divided	10	15.6
	6685.11	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Subtracted	7981.68	1296.57
16	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Divided	1	15
	7572.88	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Subtracted	8852.4	1279.52
17	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	859	14.8103
	12473	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted	11223	1250
18	26.1599	60s ribosomal protein l37a. [swissprot;acc:p12751]	Divided	305.45	11.6763
	14167	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Subtracted	15411.3	1244.3
19	26.1599	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	11.6763
	2804	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Subtracted	1593	1211
20	0.00001	ero1-like. [refseq;acc:nm_014584]	Divided	82	8200000
	7608	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Subtracted	8763	1155
21	17.6611	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	118.878	6.73106
	5690.63	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]	Subtracted	6804.88	1114.25
22	0.00001	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Divided	60	6000000
	30022.4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Subtracted	31122	1099.6
23	59	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	5900000
	5540.2	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Subtracted	6596.23	1056.03
24	158	ptd016 protein. [refseq;acc:nm_016125]	Divided	30	5.26667
	2208.1	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	3233.86	1025.76
25	773	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided	148	5.22297
	1377	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Subtracted	459.5	917.5

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.