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 951 to 1000 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
60	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Ranked	Divided	1	266.864	336.184	1.25976
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Squared		0	219.839	59.1928	3.71395
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]			1	219048	129762	1.68808
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Rooted	Subtracted		137.446	120.823	16.623
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared			192904	126167	66737
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Rooted		0	58.6947	51.8401	6.8546
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]		Divided		8.48528	12.2882	1.44818
	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]			1	35.6294	49.8119	1.39806
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Measured	Subtracted	0	5302.7	4827.7	475
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]			1	16771.5	12889.1	3882.4
61	adp-ribosylation factor 3. [swissprot;acc:p16587]	Squared	Divided	0	33.5285	123.56	3.68522
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Measured	Subtracted	1	6475.5	10307.5	3832
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]			0	870.482	403.196	467.286
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]		Divided		324.442	593.094	1.82804
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]			1	4489.19	2765.82	1.6231
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Ranked			266.864	336.182	1.25975
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Rooted			43.4291	31.7159	1.36932
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		Subtracted		137.446	120.823	16.623
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]			0	15.7225	22.5496	6.8271
	necdin. [swissprot;acc:q99608]	Squared	Divided	1	219048	129762	1.68808
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]		Subtracted	0	8107.36	10981.2	2873.84
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Ranked		1	269.248	327.642	58.394
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]			0	14463	11356	3107
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]		Divided		15352	11346.5	1.35302
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Rooted			6.63325	4.58258	1.44749
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Squared	Subtracted	1	192779	126095	66684
62	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Ranked		0	17410.5	14360	3050.5
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Measured		1	6475.5	10307.5	3832
	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Rooted	Divided	0	15.0883	21.8314	1.44691
			Subtracted				6.7431
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Measured	Divided		210.767	384.407	1.82385
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Squared			21.2079	6.15501	3.44563
	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Ranked			9418.7	12695.6	1.34791
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Measured		1	4489.19	2765.82	1.6231
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Ranked			266.865	336.181	1.25974
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted	Subtracted		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

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.