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 3758 to 3807 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
235	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured	Divided	1	5181.2	6410.58	1.23728
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Squared		0	23310.5	31089.6	1.33372
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Rooted			26.1597	29.2445	1.11792
236	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]		Subtracted		14.2752	16.6919	2.4167
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Measured			1766.66	1908.13	141.47
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Ranked		1	252.644	228.42	24.224
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Squared		0	87.2069	269.97	182.763
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Ranked			10551.1	11579.9	1028.8
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Rooted	Divided	1	137.446	120.823	1.13758
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Squared	Subtracted		41502.9	30836.8	10666.1
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Rooted			95.0526	85.3206	9.732
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Measured			9649.61	11053.5	1403.89
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]		Divided	0	2715.75	3103.01	1.1426
	pnas-18. [sptrembl;acc:q9bzu3]	Rooted			24.2086	21.6857	1.11634
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Squared			18175.2	13699.8	1.32668
	pp3111 protein. [refseq;acc:nm_022156]	Ranked		1	227.357	254.15	1.11785
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]			0	15245.4	16788.5	1.10122
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Measured		1	4723.53	5828.46	1.23392
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Squared			42411.6	55802.1	1.31573
237	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]			0	5219.15	3979.89	1.31138
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked			9984	9067	1.10114
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Rooted	Subtracted		14.2464	16.6605	2.4141
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]		Divided		21.2911	23.7622	1.11606
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]		Subtracted	1	133.216	123.627	9.589
	germ cell-less. [refseq;acc:nm_022471]	Measured		0	1829.81	1694.05	135.76
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Ranked			10551.6	11573.7	1022.1
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Rooted	Divided	1	137.446	120.823	1.13758
	metaxin 2. [swissprot;acc:o75431]	Squared	Subtracted		41236	51807	10571
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Ranked			242.011	266.18	24.169
	p28 ing5. [refseq;acc:nm_032329]	Measured	Divided	0	2551.23	2243.69	1.13707
	scribble. [refseq;acc:nm_015356]	Squared	Subtracted		4169.68	3987.55	182.13
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Measured		1	9649.61	11053.5	1403.89
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Squared	Divided		42411.6	55802.1	1.31573
	syntaxin 18. [swissprot;acc:q9p2w9]	Ranked			227.357	254.15	1.11785
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Measured			4567.04	5631.2	1.23301
238	casein kinase i alpha s-like. [refseq;acc:nm_145203]			0	2198.47	1933.94	1.13678
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Ranked			12677.7	13941.7	1.0997
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Rooted	Subtracted		14.232	16.6448	2.4128
	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	Squared		1	42566.2	52985.3	10419.1
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Ranked		0	10551.6	11573.7	1022.1
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Rooted	Divided		20.6514	18.5098	1.1157
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]			1	137.446	120.823	1.13758
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Ranked	Subtracted		252.512	228.356	24.156
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Squared	Divided		42411.6	55802.1	1.31573
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Measured			27642.5	22440.4	1.23182
	rd protein. [swissprot;acc:p18615]	Ranked			227.357	254.15	1.11785
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	Measured	Subtracted	0	494.417	359.631	134.786
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Rooted		1	56.3709	65.8949	9.524
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Measured			9649.61	11053.5	1403.89
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Squared		0	4841.65	4659.88	181.77

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.