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 751 to 800 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
47	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Measured	Subtracted	0	3645.5	3118.3	527.2
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	1	98517.9	56927.2	1.73059
48	60s acidic ribosomal protein p1. [swissprot;acc:p05386]		Subtracted	0	49458.1	54614.9	5156.8
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	Divided		870.482	403.196	2.15895
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Subtracted		999.28	481.725	517.555
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		Divided	1	779.167	1390.33	1.78438
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Ranked			65.4586	83.0461	1.26868
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared		0	960.518	176.164	5.45241
	importin 9. [refseq;acc:nm_018085]	Rooted	Subtracted		21.8651	29.828	7.9629
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Squared	Divided	1	6300.2	10703.5	1.69891
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	Subtracted		137.446	120.823	16.623
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Ranked	Divided	0	9830	6909	1.42278
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Squared	Subtracted	1	210199	136638	73561
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Ranked		0	18359.8	14447.8	3912
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Rooted	Divided	1	27.7254	44.0299	1.58807
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Subtracted		350	290	60
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Measured			24806.9	20369.9	4437
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Rooted	Divided	0	15.0533	9.31487	1.61605
49	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Squared	Subtracted		11625.2	6483.52	5141.68
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		Divided	1	28994.2	17134.8	1.69212
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Ranked			133	105	1.26667
	brain protein 16. [refseq;acc:nm_016458]			0	6890.54	4854.99	1.41927
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted	1	24806.9	20369.9	4437
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Squared			201896	131906	69990
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Ranked			350	290	60
	dead-box protein. [refseq;acc:nm_018665]			0	10628.3	14486	3857.7
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Squared	Divided		8.10857	43.7473	5.39519
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Measured	Subtracted		153	662	509
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Rooted	Divided	1	27.7254	44.0299	1.58807
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		Subtracted		137.446	120.823	16.623
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Measured	Divided		779.167	1390.33	1.78438
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Rooted	Subtracted	0	21.8651	29.828	7.9629
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]		Divided		14.1508	8.89106	1.59158
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Measured			72	151	2.09722
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Ranked		1	133	105	1.26667
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]			0	9249.73	13091.4	1.41533
			Subtracted				3841.67
	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Measured		1	24473.9	20127.8	4346.1
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked			350	290	60
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared			173408	242989	69581
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Rooted	Divided	0	11.0328	6.96286	1.58452
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]			1	27.7254	44.0299	1.58807
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Subtracted		137.446	120.823	16.623
	mstp028 protein. [refseq;acc:nm_031954]	Squared		0	105962	110835	4873
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Measured	Divided	1	779.167	1390.33	1.78438
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Squared		0	10.974	2.38124	4.60852
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]			1	28994.2	17134.8	1.69212
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Rooted	Subtracted	0	7.74597	0	7.74597
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Measured	Divided		44	21	2.09524
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]		Subtracted		4962.34	5469.68	507.34

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.