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	green	description	Network Comparison Type	Interaction Map	network_comparison	red

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Showing element 1 to 50 of 29840 in total

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

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

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.