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

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Showing element 986 to 1035 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
62	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted	Subtracted	1	137.446	120.823	16.623
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Squared	Divided		219048	129762	1.68808
	pnas-18. [sptrembl;acc:q9bzu3]		Subtracted	0	14643.9	11814.6	2829.3
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Rooted	Divided	1	43.4519	31.7522	1.36847
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Ranked	Subtracted		269.23	327.601	58.371
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Measured		0	1442	977	465
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Squared		1	189976	124480	65496
63	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	Divided	0	18.1049	12.6095	1.43581
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked		1	266.865	336.178	1.25973
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Rooted			43.4554	31.7576	1.36835
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]		Subtracted		137.446	120.823	16.623
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared	Divided		219048	129762	1.68808
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Measured			4489.19	2765.82	1.6231
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Ranked	Subtracted		260.532	204.309	56.223
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]		Divided	0	8519.83	11453	1.34428
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Measured	Subtracted		1442	977	465
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	Divided		1.24091	0.365145	3.3984
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Rooted	Subtracted		37.9737	31.257	6.7167
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared			99229.9	96418.4	2811.5
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]			1	189976	124480	65496
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Measured			6475.5	10307.5	3832
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]		Divided	0	31.1429	56.278	1.80709
		Ranked	Subtracted		18662.8	15627	3035.8
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Rooted	Divided	1	63.8686	47.2654	1.35128
	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Measured	Subtracted		6475.5	10307.5	3832
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Ranked			260.532	204.309	56.223
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared		0	14470.6	11676.7	2793.9
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]			1	144940	81169.7	63770.3
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Measured	Divided		4489.19	2765.82	1.6231
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Ranked			266.868	336.159	1.25965
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]		Subtracted	0	8152.55	11134.8	2982.25
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Measured			607	1068	461
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Squared	Divided	1	219048	129762	1.68808
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Rooted	Subtracted		137.446	120.823	16.623
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]		Divided	0	15.7225	22.5496	1.43422
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Measured			0.00001	18	1800000
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Rooted	Subtracted		37.9737	31.257	6.7167
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Ranked	Divided		15264	20387	1.33563
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Squared			50.8715	15.2519	3.33542
65	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]				50.642	15.1833	3.33538
	60s ribosomal protein l21. [swissprot;acc:p46778]	Rooted			20.5734	29.2291	1.42072
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Measured	Subtracted	1	22515.5	18702.6	3812.9
	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Ranked	Divided	0	7853.67	10406.3	1.32502
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Rooted		1	63.8686	47.2654	1.35128
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Ranked			267.136	336.077	1.25807
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared			219048	129762	1.68808
	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]	Rooted	Subtracted		137.446	120.823	16.623
	metaxin 1. [swissprot;acc:q13505]	Squared		0	6149.89	3429.64	2720.25
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]			1	144912	81155	63757
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Measured		0	420.365	861.814	441.449

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.