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

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Showing element 1001 to 1050 of 9634 in total

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

Rank	description	Interaction Map	green	red	network_comparison
501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	High confidence	0.00001	0.00001	1
	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]	Low confidence	1225.02	1298.24	1.05977
502	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]		5516.84	5846.15	1.05969
	brca1 associated protein. [refseq;acc:nm_006768]	High confidence	0.00001	0.00001	1
503	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Low confidence	1895.34	1788.69	1.05962
504	g protein pathway suppressor 2 (gps2 protein). [swissprot;acc:q13227]		569	537	1.05959
505	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]		1913.73	2027.06	1.05922
506	dead-box protein 3, y-chromosomal. [swissprot;acc:o15523]		2301.01	2437.08	1.05913
507	pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5]		779.665	825.575	1.05888
508	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		1951.18	2065.68	1.05868
509	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]		4610.93	4881.38	1.05865
510	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]		2837.1	2680.03	1.05861
511	p28 ing5. [refseq;acc:nm_032329]		3631.3	3842.88	1.05827
512	brain protein 16. [refseq;acc:nm_016458]		2837.61	3002.7	1.05818
513	40s ribosomal protein s10. [swissprot;acc:p46783]		1135.73	1201.47	1.05788
514	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]		16295.1	17235.5	1.05771
515	ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39]		1134.29	1199.57	1.05755
516	60s ribosomal protein l18a. [swissprot;acc:q02543]		3920.97	3708.61	1.05726
517	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]		1311.25	1385.47	1.0566
518	cytochrome c oxidase subunit viia-l related protein, mitochondrial precursor. [swissprot;acc:o60397]		1279.26	1351.4	1.05639
519	keratin associated protein 9.2. [refseq;acc:nm_031961]		958.097	1011.61	1.05585
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]		2192.97	2077.04	1.05582
522	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]		958.728	1011.83	1.05539
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]		958.732		1.05538
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]		958.753		1.05537
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]		2312.27	2439.81	1.05516
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]		740.494	781.187	1.05495
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]		1284.05	1354.59	1.05494
536	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]		959.463	1012.08	1.05484
537	inositol polyphosphate-5-phosphatase, 145kda; hp51cn; inositol polyphosphate-5-phosphatase, 145kd. [refseq;acc:nm_005541]		1245.48	1180.86	1.05472
538	aldehyde dehydrogenase, dimeric nadp-preferring (ec 1.2.1.5) (aldh class 3) (aldhiii). [swissprot;acc:p30838]		1224.9	1161.52	1.05457
539	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]		1926.2	1826.57	1.05454
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]		2227.75	2112.62	1.0545
541	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]		3969.94	4185.81	1.05438
542	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]		2405.01	2535.07	1.05408
543	dna-crosslink repair gene snm1. [refseq;acc:nm_014881]		2519.99	2656.05	1.05399
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]		1941.08	1842.35	1.05359
546	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]		644.464	611.712	1.05354
547	mbt domain containing 1. [refseq;acc:nm_017643]		756.852	797.368	1.05353
548	lactotransferrin precursor (lactoferrin) [contains: lactoferroxin a; lactoferroxin b; lactoferroxin c]. [swissprot;acc:p02788]		888.843	935.913	1.05296

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.