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

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Showing element 601 to 650 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Filtered	Interaction Map	Value Type	green	red	network_comparison
38	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	0	Low confidence	Measured	35.5	105.5	2.97183
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]			Rooted	5.80679	9.84765	1.69589
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	High confidence	Ranked	253	322	1.27273
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]			Squared	192141	106226	1.80879
	rab11-family interacting protein 4. [refseq;acc:nm_032932]		Low confidence	Measured	8696.7	7407.56	1.17403
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	0	High confidence	Rooted	6.97663	3.62029	1.92709
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]		Low confidence	Ranked	9243.55	6768.72	1.36563
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]		High confidence	Measured	120.429	320.012	2.65727
39	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]		Low confidence	Ranked	8270.5	11290	1.36509
	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	1		Rooted	55.8176	63.4164	1.13614
	eferin. [swissprot;acc:o75154]			Measured	8696.7	7407.56	1.17403
	ero1-like. [refseq;acc:nm_014584]	0	High confidence	Ranked	20536	13853	1.48242
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	1	Low confidence		282.937	247.202	1.14456
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]		High confidence	Measured	907.903	1836.8	2.02312
				Rooted	24.37	40.28	1.65285
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0	Low confidence	Squared	0.355148	3.41692	9.62112
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]			Measured	35.5	105.5	2.97183
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1		Squared	61881.5	82347.8	1.33073
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0		Rooted	5.80678	9.84765	1.69589
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]		High confidence	Measured	192.295	482.426	2.50878
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1		Squared	192141	106226	1.80879
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	0		Rooted	14.4058	7.90063	1.82337
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1		Ranked	253	322	1.27273
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	0		Squared	5.33358	43.8625	8.22384
40	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]			Rooted	13.5647	24.454	1.80277
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1		Squared	81169.7	144940	1.78564
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]			Ranked	253	322	1.27273
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	0			5699	3845	1.48218
	fos-related antigen 2. [swissprot;acc:p15408]	1	Low confidence	Measured	7600.25	6480.59	1.17277
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0		Ranked	15924	11761	1.35397
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	1	High confidence	Measured	907.978	1836.81	2.02297
				Rooted	24.3705	40.2797	1.65281
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0		Squared	0.742249	5.83408	7.86
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		Low confidence	Measured	35.5	105.5	2.97183
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]			Rooted	5.80678	9.84765	1.69589
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1		Squared	61881.5	82347.8	1.33073
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	0			0.355148	3.41692	9.62112
	nanos (fragment). [sptrembl;acc:q8wy41]		High confidence	Measured	151	377	2.49669
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	Low confidence	Rooted	63.2842	55.7075	1.13601
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]			Ranked	223.538	255.382	1.14245
41	60s ribosomal protein l21. [swissprot;acc:p46778]	0	High confidence		6758.83	9994.33	1.47871
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	1	Low confidence		200.55	228.147	1.13761
	dystrophin. [swissprot;acc:p11532]	0	High confidence	Squared	12.5624	98.4011	7.83299
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	1		Measured	907.978	1836.81	2.02297
				Rooted	24.3705	40.2797	1.65281
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0	Low confidence	Measured	35.5	105.5	2.97183
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	1		Squared	61881.5	82347.8	1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0		Rooted	5.80678	9.84765	1.69589
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]			Squared	0.355148	3.41692	9.62112
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1		Rooted	63.2842	55.7075	1.13601

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.