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	red	Interaction Map	Filtered	green	network_comparison

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Showing element 101 to 150 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	Interaction Map	green	network_comparison
7	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted	310840	High confidence	442993	132153
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Ranked	Divided	318	Low confidence	240	1.325
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Measured		736.5		2113.5	2.86965
		Ranked	Subtracted	318		240	78
		Squared	Divided	128.386		1057.25	8.23493
		Rooted		27.1385		45.9728	1.69401
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		Subtracted	145.551	High confidence	168.796	23.245
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked		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]	Measured	Divided	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]	Measured	Subtracted	36360.3	Low confidence	43368.8	7008.5
8	db83 protein. [swissprot;acc:p57088]		Divided	1153.5	High confidence	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]	Measured	Subtracted	33111.4	Low confidence	39358.1	6246.7
		Squared		250303	High confidence	354894	104591
	hbs1-like. [refseq;acc:nm_006620]	Ranked	Divided	215		322	1.49767
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		Subtracted	288		362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared		106226	Low confidence	192141	85915
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Rooted		27.1385		45.9728	18.8343
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Ranked	Divided	318		240	1.325
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured	Subtracted	21185	High confidence	28492	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted		145.551		168.796	23.245
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Measured	Divided	3278	Low confidence	5058.5	1.54317
		Squared		2543.26		6056.43	2.38136
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Ranked	Subtracted	305.472		247.246	58.226
		Rooted	Divided	31.8641		47.6922	1.49674
9	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Ranked		58		44	1.31818
	gbp protein isoform a. [refseq;acc:nm_017870]		Subtracted	305.399		247.213	58.186
		Rooted	Divided	31.8923		47.7107	1.49599
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked	Subtracted	288	High confidence	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted		145.551		168.796	23.245
	n33 protein. [swissprot;acc:q13454]	Measured	Divided	3278	Low confidence	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]	Rooted	Subtracted	27.1385		45.9728	18.8343
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		21185	High confidence	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared		256169		162517	93652
	sperm associated antigen 7. [refseq;acc:nm_004890]	Measured		23318	Low confidence	19280.8	4037.2
		Squared		209554		136572	72982
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	Divided	398.5	High confidence	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]	Ranked		212		309	1.45755
10	implantation-associated protein. [refseq;acc:nm_032121]	Measured		3278	Low confidence	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]	Ranked	Subtracted	305.303		247.169	58.134
		Rooted	Divided	31.9296		47.7352	1.49501
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	219048	High confidence	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Ranked	Divided	58	Low confidence	44	1.31818

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.