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 2325 to 2374 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
146	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	Divided	0	13.9593	11.8643	1.17658
	huntingtin interacting protein c. [refseq;acc:nm_012272]			1	55.0737	66.0298	1.19894
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	Subtracted	0	960.518	176.164	784.354
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Ranked	Divided	1	265.632	319.531	1.20291
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Subtracted	0	3208.8	4871.6	1662.8
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted		1	41.6734	28.9323	12.7411
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Squared	Divided		103496	146848	1.41888
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Rooted	Subtracted	0	11.6322	7.84538	3.78682
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Squared		1	86281	65058.3	21222.7
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Ranked			239.336	267.879	28.543
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	0	8.15919	4.74982	1.71779
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	Subtracted	1	2671	871	1800
147	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked	Divided	0	11080.3	9505.89	1.16562
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Rooted			21.8452	18.5801	1.17573
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]		Subtracted	1	41.6851	28.9509	12.7342
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Measured	Divided	0	292.152	378.206	1.29455
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Rooted		1	42.0574	50.4237	1.19893
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Squared	Subtracted		55630.4	76083.7	20453.3
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Ranked			239.32	267.842	28.522
	nanos (fragment). [sptrembl;acc:q8wy41]	Measured		0	377	151	226
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	Divided	1	50.7983	42.3003	1.2009
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Squared	Subtracted	0	9106.26	9878.65	772.39
		Rooted			31.7569	27.9904	3.7665
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Squared	Divided		180.799	307.058	1.69834
	protein x 0004. [refseq;acc:nm_016301]	Measured	Subtracted	1	2671	871	1800
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]		Divided		11068	8508.5	1.30082
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Squared			103496	146848	1.41888
	tubby protein homolog. [swissprot;acc:p50607]	Ranked	Subtracted	0	12303.7	10641.7	1662
148	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Measured	Divided	1	11068	8508.5	1.30082
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Squared		0	699.353	414.113	1.6888
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Measured			293.178	379.474	1.29435
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Ranked	Subtracted		7706.5	6058	1648.5
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]			1	226.582	198.444	28.138
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Rooted	Divided	0	8.52047	10.0173	1.17567
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]			1	42.0577	50.424	1.19892
	p28 ing5. [refseq;acc:nm_032329]		Subtracted	0	32.711	36.4589	3.7479
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]			1	41.6879	28.9554	12.7325
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Measured		0	1249.24	1023.76	225.48
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	Divided	1	103496	146848	1.41888
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]		Subtracted		70011	49783	20228
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked	Divided		296.677	247.559	1.19841
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	Subtracted	0	978.105	1746.18	768.075
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Ranked	Divided		6755.71	7863.63	1.164
	symplekin. [swissprot;acc:q92797]	Measured	Subtracted	1	15213.4	13418.1	1795.3
149	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Squared		0	2783.53	3517.26	733.73
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]		Divided	1	103496	146848	1.41888
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked			142	170	1.19718
	block 23. [sptrembl;acc:q8nhw5]			0	11469.3	13334.8	1.16265
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Measured			293.178	379.474	1.29435
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted		1	42.0684	50.4323	1.19882

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.