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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Rank	Gene	Hugo	description	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2101 to 2150 of 66312 in total

Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
132	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	Measured	Low confidence	7030.67	7794.8	764.13
				Ranked		203.016	189.965	13.051
	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Divided	Measured	High confidence	2236.61	2980.35	1.33253
	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]		Rooted		44.963	55.0576	1.22451
	HPRT1	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]		Squared	Low confidence	65137.2	73946.3	1.13524
	MAP2K4	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]		Measured		5948.88	5441.83	1.09318
	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	Ranked	High confidence	229.406	196.695	32.711
	PTPRB	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]		Squared		71062.2	95488.6	24426.4
	RBM10	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]			Low confidence	67930.9	60946.6	6984.3
	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]		Rooted	High confidence	144.606	157.824	13.218
	TGM1	protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735]	Divided		Low confidence	63.8063	68.4797	1.07324
	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		Ranked	High confidence	350	290	1.2069
133	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Subtracted			226.887	194.72	32.167
		ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Divided	Measured	Low confidence	7013	7662.77	1.09265
	ABRA	striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166]		Rooted		65.2217	69.9574	1.07261
	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Subtracted		High confidence	144.606	157.824	13.218
	BBS9	pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451]	Divided	Squared	Low confidence	55849.9	49199.6	1.13517
	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Subtracted	Measured	High confidence	12798.9	10887.2	1911.7
	DVL2	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]			Low confidence	7034.43	7797.14	762.71
				Ranked		203.007	189.985	13.022
	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]		Rooted		64.712	69.8815	5.1695
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	Measured	High confidence	23421.5	17580.4	1.33225
	INADL	inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799]	Subtracted	Squared	Low confidence	67882.7	60913.7	6969
	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Divided	Rooted	High confidence	45.4558	55.5995	1.22316
	PROM1	prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490]		Ranked	Low confidence	220.268	206.997	1.06411
	PRSS16	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Subtracted	Squared	High confidence	71062.2	95488.6	24426.4
	TMEM132A	gbp protein isoform a. [refseq;acc:nm_017870]	Divided			1182.25	1726.55	1.46039
	TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]		Ranked		350	290	1.2069
134	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		Measured		21785.2	16426.1	1.32626
		huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Subtracted	Ranked		226.884	194.79	32.094
		transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802]			Low confidence	218.36	205.4	12.96
	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Divided	Rooted		64.1512	68.7584	1.07182
	CCDC47	gk001 protein. [refseq;acc:nm_020198]	Subtracted	Squared	High confidence	71062.2	95488.6	24426.4
	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]		Measured		12796.8	10886	1910.8
	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Divided	Ranked		350	290	1.2069
	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Subtracted	Measured	Low confidence	7054.1	7809.38	755.28
	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]		Rooted		64.712	69.8815	5.1695
	GATAD2A	p66 alpha. [refseq;acc:nm_017660]	Divided	Squared	High confidence	81888.8	56306.5	1.45434
	GSTO2	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]		Measured	Low confidence	6670.21	7286.66	1.09242
	MPDZ	multiple pdz domain protein. [refseq;acc:nm_003829]	Subtracted	Squared		67876.4	60909.3	6967.1
	NHLH1	helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575]	Divided			55838.6	49199.4	1.13494
	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]		Rooted	High confidence	44.849	54.7964	1.2218
	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Subtracted			54.8203	67.934	13.1137
	TAGLN	transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995]	Divided	Ranked	Low confidence	218.561	205.431	1.06391
135	AADAT	alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228]	Subtracted	Measured		9986.51	10741.3	754.79
	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Divided		High confidence	21785.2	16426.1	1.32626
	CACNG8	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Subtracted	Rooted		49.2923	62.3969	13.1046
	CAPN2	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Divided		Low confidence	64.1536	68.7605	1.07181
	CLSTN2	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Subtracted	Squared	High confidence	71033.4	95440.2	24406.8
	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	Ranked		350	290	1.2069

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.