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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

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

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

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.