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 218 to 267 of 3730 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	1	4366.44	5899.76	1.35116
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	0	1833	2637	1.43863
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	1	4366.44	5899.76	1.35116
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	0	2965.5	2063	1.43747
112	lats homolog 1. [refseq;acc:nm_004690]		160	112.25	1.42539
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	1	4366.44	5899.76	1.35116
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	0	160	112.25	1.42539
114	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]		671.769	472.945	1.4204
	huntingtin interacting protein c. [refseq;acc:nm_012272]	1	4300.47	5807.72	1.35048
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		21185	28492	1.34491
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	0	385	543	1.41039
116	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		668	475	1.40632
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	1	21185	28492	1.34491
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	0	170.5	122	1.39754
118	methyltransferase like 2. [refseq;acc:nm_018396]		31	43	1.3871
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	21185	28492	1.34491
119	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	0	633.85	460.2	1.37734
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	21185	28492	1.34491
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]		5136.78	6895.98	1.34247
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	0	494.417	359.631	1.37479
121	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]		19.6667	14.3333	1.3721
	transcription factor jun-b. [swissprot;acc:p17275]	1	5579.18	7488.4	1.3422
122	high-mobility group 20a. [refseq;acc:nm_018200]		5140.14	6893.53	1.34112
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	0	107	78	1.37179
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1	24260.3	18172.1	1.33503
	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]	0	2285.62	1681.3	1.35944
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	1	24255.7	18168.9	1.33501
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	0	3248.95	2399.76	1.35386
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	1	24255.7	18168.9	1.33501
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	0	1095.42	812.166	1.34876
126	calcyphosine. [swissprot;acc:q13938]		472.524	635.875	1.3457
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1	24250	18164.9	1.33499
127	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	0	86	64	1.34375
	transcription factor jun-d. [swissprot;acc:p17535]	1	5638.2	7523.39	1.33436
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]		4355.61	5810.82	1.3341
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	0	81.504	60.8613	1.33918
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	1	4358.13	5811.49	1.33348
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	0	606.485	454.837	1.33341
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	1	2234.68	2978.53	1.33287
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	0	42	56	1.33333
131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	1	2234.73	2978.57	1.33285
	serpin b11. [swissprot;acc:q96p15]	0	42	56	1.33333
132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	1	2236.61	2980.35	1.33253
133	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]	0	252	335	1.32937
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	1	23421.5	17580.4	1.33225
134	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		21785.2	16426.1	1.32626

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.