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 2477 to 2526 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
155	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Squared	Divided	0	21273.2	12858.5	1.65441
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Ranked	Subtracted		13248.5	11666.4	1582.1
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Rooted	Divided	1	55.7423	65.6839	1.17835
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	Measured		0	2230.13	1729.7	1.28932
156	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Squared	Subtracted		2785.55	3421.01	635.46
	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]			1	70525.9	52678.7	17847.2
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Rooted	Divided	0	14.2464	16.6605	1.16945
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Subtracted	1	55.1026	67.5701	12.4675
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured	Divided		23693.7	18263	1.29736
	metaxin 1. [swissprot;acc:q13505]		Subtracted	0	933.395	723.368	210.027
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]			1	9035	7279.6	1755.4
	nuclear protein ukp68. [refseq;acc:nm_024824]	Ranked			227.491	199.458	28.033
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Squared	Divided	0	366.272	222.124	1.64895
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Ranked		1	249.663	298.263	1.19466
	septin 10 isoform 1. [refseq;acc:nm_144710]	Squared			89578.7	125883	1.40528
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Rooted			56.3447	66.124	1.17356
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Ranked	Subtracted	0	13248.5	11666.4	1582.1
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Rooted			39.5626	36.099	3.4636
	tubby protein homolog. [swissprot;acc:p50607]	Ranked	Divided		12303.7	10641.7	1.15618
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Measured			2230.13	1729.7	1.28932
157	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Squared	Subtracted		2569.37	3201.81	632.44
	brain protein 44. [swissprot;acc:o95563]		Divided	1	89182.8	125229	1.40418
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Rooted		0	14.2752	16.6919	1.16929
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]			1	52.7582	61.9123	1.17351
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Measured			23693.7	18263	1.29736
	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	Squared	Subtracted		76438	58889.7	17548.3
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted			55.1113	67.5537	12.4424
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked		0	11364	12941	1577
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured	Divided		261.105	336.584	1.28908
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]		Subtracted	1	9035	7279.6	1755.4
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Ranked			312	284	28
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Measured		0	1843	1633	210
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Rooted			3.62029	6.97663	3.35634
	transcription factor lbx1. [swissprot;acc:p52954]	Ranked	Divided	1	249.663	298.263	1.19466
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]			0	18079	15652	1.15506
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Squared			6123.28	3763.18	1.62716
158	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked	Subtracted		11080.3	9505.89	1574.41
	60s ribosomal protein l9. [swissprot;acc:p32969]	Measured			1685.44	1894.01	208.57
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Rooted	Divided	1	56.3507	66.1252	1.17346
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Ranked	Subtracted		312	284	28
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Rooted	Divided	0	14.2752	16.6919	1.16929
	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	Squared	Subtracted	1	76360.8	58841.7	17519.1
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Measured	Divided	0	1283.48	1649.37	1.28508
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Squared	Subtracted		18476.6	19091.9	615.3
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	Divided	1	23693.7	18263	1.29736
	mosaic protein lgn. [swissprot;acc:p81274]	Ranked			249.663	298.263	1.19466
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Measured	Subtracted		9035	7279.6	1755.4
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Rooted			149.397	136.972	12.425
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Ranked	Divided	0	10060.2	11616.4	1.15469
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Rooted	Subtracted		41.5652	38.2237	3.3415

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.