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	Filtered	Rank	description	Network Comparison Type	network_comparison	Interaction Map	green	red

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Showing element 1001 to 1050 of 38536 in total

Value Type  : Measured
Filtered  : 0
Network Comparison Type  : Divided

Rank	description	network_comparison	Interaction Map	green	red
501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	1	High confidence	0.00001	0.00001
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	1.05977	Low confidence	1225.02	1298.24
502	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	1.05969		5516.84	5846.15
	brca1 associated protein. [refseq;acc:nm_006768]	1	High confidence	0.00001	0.00001
503	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	1.05962	Low confidence	1895.34	1788.69
504	g protein pathway suppressor 2 (gps2 protein). [swissprot;acc:q13227]	1.05959		569	537
505	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1.05922		1913.73	2027.06
506	dead-box protein 3, y-chromosomal. [swissprot;acc:o15523]	1.05913		2301.01	2437.08
507	pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5]	1.05888		779.665	825.575
508	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	1.05868		1951.18	2065.68
509	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	1.05865		4610.93	4881.38
510	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	1.05861		2837.1	2680.03
511	p28 ing5. [refseq;acc:nm_032329]	1.05827		3631.3	3842.88
512	brain protein 16. [refseq;acc:nm_016458]	1.05818		2837.61	3002.7
513	40s ribosomal protein s10. [swissprot;acc:p46783]	1.05788		1135.73	1201.47
514	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	1.05771		16295.1	17235.5
515	ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39]	1.05755		1134.29	1199.57
516	60s ribosomal protein l18a. [swissprot;acc:q02543]	1.05726		3920.97	3708.61
517	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	1.0566		1311.25	1385.47
518	cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397]	1.05639		1279.26	1351.4
519	keratin associated protein 9.2. [refseq;acc:nm_031961]	1.05585		958.097	1011.61
520	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]			402.138	380.866
521	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	1.05582		2192.97	2077.04
522	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	1.05539		958.728	1011.83
523	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]			958.724
524	keratin associated protein 1.5. [refseq;acc:nm_031957]			958.726
525	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
526	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]			958.728
527	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	1.05538		958.732
528	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]			958.748	1011.84
529	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]			958.749
530	similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230]	1.05537		958.753
531	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]			958.745	1011.83
532	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
533	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	1.05516		2312.27	2439.81
534	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	1.05495		740.494	781.187
535	cytochrome c oxidase polypeptide viia-heart, mitochondrial precursor (ec 1.9.3.1) (cytochrome c oxidase subunit viia-h) (cox viia-m). [swissprot;acc:p24310]	1.05494		1284.05	1354.59
536	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	1.05484		959.463	1012.08
537	inositol polyphosphate-5-phosphatase, 145kda; hp51cn; inositol polyphosphate-5-phosphatase, 145kd. [refseq;acc:nm_005541]	1.05472		1245.48	1180.86
538	aldehyde dehydrogenase, dimeric nadp-preferring (ec 1.2.1.5) (aldh class 3) (aldhiii). [swissprot;acc:p30838]	1.05457		1224.9	1161.52
539	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	1.05454		1926.2	1826.57
540	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	1.0545		2227.75	2112.62
541	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	1.05438		3969.94	4185.81
542	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	1.05408		2405.01	2535.07
543	dna-crosslink repair gene snm1. [refseq;acc:nm_014881]	1.05399		2519.99	2656.05
544	t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283]
545	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	1.05359		1941.08	1842.35
546	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	1.05354		644.464	611.712
547	mbt domain containing 1. [refseq;acc:nm_017643]	1.05353		756.852	797.368
548	lactotransferrin precursor (lactoferrin) [contains: lactoferroxin a; lactoferroxin b; lactoferroxin c]. [swissprot;acc:p02788]	1.05296		888.843	935.913

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.