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

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Showing element 601 to 650 of 66312 in total

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Rank	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
38	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Divided	Squared	Low confidence	82347.8	61881.5	1.33073
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Subtracted	Measured	High confidence	23693.7	18263	5430.7
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Squared	Low confidence	82347.8	61881.5	20466.3
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	Ranked	High confidence	322	253	1.27273
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		Squared		106226	192141	1.80879
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted	Rooted		26.0288	43.1914	17.1626
	rab11-family interacting protein 4. [refseq;acc:nm_032932]	Divided	Measured	Low confidence	7407.56	8696.7	1.17403
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	Squared	High confidence	226186	145568	80618
39	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
	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]	Divided	Rooted	Low confidence	63.4164	55.8176	1.13614
	eferin. [swissprot;acc:o75154]		Measured		7407.56	8696.7	1.17403
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Subtracted	Rooted	High confidence	26.0288	43.1914	17.1626
	fos-related antigen 2. [swissprot;acc:p15408]			Low confidence	66.6469	75.3812	8.7343
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Divided	Ranked		247.202	282.937	1.14456
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]		Measured	High confidence	1836.8	907.903	2.02312
			Rooted		40.28	24.37	1.65285
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Subtracted	Ranked		268.565	334.483	65.918
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		Squared	Low confidence	82347.8	61881.5	20466.3
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]		Measured		12176.9	13781.8	1604.9
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Divided	Squared		82347.8	61881.5	1.33073
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Subtracted	Measured	High confidence	23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Divided	Squared		106226	192141	1.80879
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Ranked		322	253	1.27273
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Subtracted		Low confidence	234.802	260.98	26.178
40	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]		Squared	High confidence	222655	143584	79071
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Divided			144940	81169.7	1.78564
	db83 protein. [swissprot;acc:p57088]	Subtracted	Ranked	Low confidence	234.802	260.98	26.178
	deltex 2. [refseq;acc:nm_020892]			High confidence	333.144	267.393	65.751
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Divided			322	253	1.27273
	fos-related antigen 2. [swissprot;acc:p15408]		Measured	Low confidence	6480.59	7600.25	1.17277
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]			High confidence	1836.81	907.978	2.02297
			Rooted		40.2797	24.3705	1.65281
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Subtracted	Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Divided					1.33073
	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]	Subtracted	Measured	High confidence	23693.7	18263	5430.7
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]			Low confidence	736.5	2113.5	1377
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]		Rooted		66.6504	75.3798	8.7294
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided			55.7075	63.2842	1.13601
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Subtracted		High confidence	26.0288	43.1914	17.1626
	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]	Divided	Ranked	Low confidence	255.382	223.538	1.14245
41	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]				228.147	200.55	1.13761
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Subtracted		High confidence	332.925	267.274	65.651
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]		Squared		214143	138337	75806
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		Rooted	Low confidence	66.6623	75.3751	8.7128
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Divided	Measured	High confidence	1836.81	907.978	2.02297
			Rooted		40.2797	24.3705	1.65281
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		Squared	Low confidence	82347.8	61881.5	1.33073
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]		Rooted		55.7075	63.2842	1.13601
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		Squared	High confidence	144912	81155	1.78562
	necdin. [swissprot;acc:q99608]	Subtracted		Low confidence	82347.8	61881.5	20466.3

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.