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

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Showing element 3180 to 3229 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
199	Squared	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	0	7130.54	Low confidence	1.34996	9625.93
	Rooted	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]		22.6924		1.13383	20.0139
		keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]		23.8722	High confidence	1.1404	20.9331
		source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	1	61.2893		1.14842	70.3856
		tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]		70.8512	Low confidence	1.06097	75.1709
200	Measured	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		4808.79	High confidence	1.26315	6074.21
		dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	0	578.056		1.19755	482.7
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	6926.74	Low confidence	1.07324	7434.04
		zinc finger protein 267 (zinc finger protein hzf2). [swissprot;acc:q14586]	0	2350.86		1.19455	1967.99
	Ranked	alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]	1	219.543		1.05111	208.868
		egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]		242.718	High confidence	1.1372	276.018
		peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	0	8786.74		1.11644	7870.3
		zinc finger protein 221. [swissprot;acc:q9uk13]		4251.37	Low confidence	1.14033	4847.95
	Squared	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	1	54179.7		1.10772	48910.9
		gk001 protein. [refseq;acc:nm_020198]		71062.2	High confidence	1.34373	95488.6
		guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895]	0	2610.94	Low confidence	1.34821	3520.09
		transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]		5317.39	High confidence	1.42249	3738.08
	Rooted	60s ribosomal protein l27. [swissprot;acc:p08526]	1	69.691	Low confidence	1.06095	73.939
		cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	0	20.6112		1.13254	23.3431
		keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		23.8722	High confidence	1.14039	20.9333
		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	1	61.2893		1.14842	70.3856
201	Measured	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]		10392.7	Low confidence	1.07323	9683.56
		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]	0	6804.88	High confidence	1.1958	5690.63
		t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1	4810.22		1.26294	6075.04
		zinc finger protein 180 (hhz168). [swissprot;acc:q9ujw8]	0	2350.86	Low confidence	1.19455	1967.99
	Ranked	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	1	208.591		1.051	219.23
		maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	0	16853	High confidence	1.1144	15123
		splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	1	240.133		1.13601	211.382
		zinc finger protein 197 (znf20). [swissprot;acc:o14709]	0	4251.62	Low confidence	1.14032	4848.21
	Squared	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		351.996	High confidence	1.41813	499.177
		calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	1	71033.4		1.3436	95440.2
		hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]		52176.8	Low confidence	1.10771	47103.2
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	0	13924.6		1.33509	18590.6
	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	1	71.1262		1.06076	75.4476
		dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]		61.2893	High confidence	1.14842	70.3856
		keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	0	23.8722		1.14038	20.9336
		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]		58.6947	Low confidence	1.13223	51.8401
202	Measured	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]		606.049	High confidence	1.19421	723.75
		enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	1	4812.01		1.26269	6076.09
		raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]		10391.8	Low confidence	1.0732	9682.99
		zinc finger protein 28 homolog (zfp-28) (kruppel-like zinc finger factor x6). [swissprot;acc:q8nhy6]	0	2350.92		1.19455	1968.04
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1	211.51		1.05079	222.252
		serpin b11. [swissprot;acc:q96p15]	0	16853	High confidence	1.1144	15123
		short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	1	201.478		1.13553	228.784
		similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_033196]	0	4251.62	Low confidence	1.14032	4848.21
	Squared	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	1	71030.1	High confidence	1.34358	95434.8
		dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	0	3339.18		1.41433	2360.97
		phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]	1	55537.3	Low confidence	1.10765	50139.7
		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	0	23310.5		1.33372	31089.6
	Rooted	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	1	71.0652		1.06067	75.377

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.