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

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Showing element 108 to 157 of 66312 in total

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Rank	description	Network Comparison Type	Hugo	Value Type	Interaction Map	red	green	network_comparison
7	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	UFC1	Ranked	High confidence	288.754	212.554	76.2
	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]	Divided	SMPD2	Measured		1153.5	339.5	3.39764
				Squared		314.926	27.2805	11.544
				Rooted		33.9632	18.4255	1.84327
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Subtracted	BEST2	Measured	Low confidence	36360.3	43368.8	7008.5
8	db83 protein. [swissprot;acc:p57088]	Divided	TMEM33		High confidence	1153.5	339.5	3.39764
				Squared		314.926	27.2805	11.544
				Rooted		33.9632	18.4255	1.84327
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	DNASE2B	Measured	Low confidence	33111.4	39358.1	6246.7
				Squared	High confidence	250303	354894	104591
	hbs1-like. [refseq;acc:nm_006620]	Divided	HBS1L	Ranked		215	322	1.49767
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	JPH3			288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		SLC25A43	Squared	Low confidence	106226	192141	85915
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		OSBPL6	Rooted		27.1385	45.9728	18.8343
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Divided	OSBPL7	Ranked		318	240	1.325
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	PANK1	Measured	High confidence	21185	28492	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		PANK3	Rooted		145.551	168.796	23.245
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Divided	PIGF	Measured	Low confidence	3278	5058.5	1.54317
				Squared		2543.26	6056.43	2.38136
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]		JMJD1C	Rooted		31.8641	47.6922	1.49674
		Subtracted		Ranked		305.472	247.246	58.226
9	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided	MRPS17			58	44	1.31818
	gbp protein isoform a. [refseq;acc:nm_017870]		TMEM132A	Rooted		31.8923	47.7107	1.49599
		Subtracted		Ranked		305.399	247.213	58.186
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		JPH2		High confidence	288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		SLC25A43	Rooted		145.551	168.796	23.245
	n33 protein. [swissprot;acc:q13454]	Divided	TUSC3	Measured	Low confidence	3278	5058.5	1.54317
				Squared		2543.26	6056.43	2.38136
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Subtracted	OSBPL3	Rooted		27.1385	45.9728	18.8343
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		PANK2	Measured	High confidence	21185	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		PPP1R7	Squared		256169	162517	93652
	sperm associated antigen 7. [refseq;acc:nm_004890]		SPAG7	Measured	Low confidence	23318	19280.8	4037.2
				Squared		209554	136572	72982
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	TOB2	Measured	High confidence	398.5	1281.5	3.21581
				Squared		37.5863	388.696	10.3414
				Rooted		19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		XAB1	Ranked		212	309	1.45755
10	implantation-associated protein. [refseq;acc:nm_032121]		no value	Measured	Low confidence	3278	5058.5	1.54317
				Squared		2543.26	6056.43	2.38136
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]		JMJD1A	Rooted		31.9296	47.7352	1.49501
		Subtracted		Ranked		305.303	247.169	58.134
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		MAGED4	Squared	High confidence	219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Divided	SLC25A43	Ranked	Low confidence	58	44	1.31818
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Subtracted	OSBPL7	Rooted		27.1385	45.9728	18.8343
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		PANK3	Measured	High confidence	21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	Divided	ATPBD1C	Ranked		212	309	1.45755
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	UBAC1	Measured	Low confidence	19498.1	17265.4	2232.7
				Squared		189688	134787	54901
	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]		SMPD2	Ranked	High confidence	288	362	74
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	TOB1	Measured		398.5	1281.5	3.21581

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
- Hugo is the HGNC identifier if it exists
- 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.