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 2023 to 2072 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
127	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Squared	Subtracted	0	25936.7	26909.5	972.8
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	Divided	1	60.9353	75.094	1.23236
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	Subtracted		71386.9	96032.5	24645.6
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Measured	Divided	0	86	64	1.34375
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked		1	94	114	1.21277
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Rooted		0	37.9737	31.257	1.21489
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	Subtracted	1	450.5	2394.5	1944
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Squared	Divided	0	799.337	432.882	1.84655
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Ranked			9411.34	11119.7	1.18152
	transcription factor jun-d. [swissprot;acc:p17535]	Measured		1	5638.2	7523.39	1.33436
128	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Squared	Subtracted	0	3687.69	4640.77	953.08
	60s ribosomal protein l39. [swissprot;acc:p02404]	Ranked	Divided		11564.4	9794.29	1.18073
	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Squared	Subtracted	1	71346.6	95965.1	24618.5
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	Divided		94	114	1.21277
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared		0	166.774	90.363	1.8456
	importin 9. [refseq;acc:nm_018085]	Measured	Subtracted		1143.55	1397.66	254.11
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]		Divided	1	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
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Rooted	Subtracted	1	54.6527	67.9743	13.3216
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]		Divided	0	37.9737	31.257	1.21489
	pnas-18. [sptrembl;acc:q9bzu3]	Squared		1	87787.3	58155.8	1.50952
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Ranked	Subtracted		285.684	252.234	33.45
	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	9722.71	11493.8	1771.09
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Measured		1	11004.2	12944.2	1940
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	Divided		48.0515	39.0445	1.23069
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]		Subtracted	0	32.4121	28.377	4.0351
129	60s ribosomal protein l39. [swissprot;acc:p02404]	Ranked			11564.4	9794.29	1770.11
	cullin homolog 1 (cul-1). [swissprot;acc:q13616]			1	285.684	252.234	33.45
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared	Divided	0	21723.1	39570.4	1.82158
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted		1	54.2343	66.7323	1.23044
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Squared	Subtracted	0	3687.33	4640.32	952.99
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Ranked	Divided		14222.5	12058.6	1.17945
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured		1	4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked			94	114	1.21277
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Rooted	Subtracted		54.6625	67.9477	13.2852
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Measured		0	1143.55	1397.66	254.11
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Rooted	Divided		27.8028	22.9122	1.21345
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared		1	178263	118639	1.50257
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured		0	606.485	454.837	1.33341
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]		Subtracted	1	15274.9	13346.9	1928
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Squared			71062.4	95488.9	24426.5
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Rooted		0	32.4121	28.377	4.0351
130	44050 protein. [refseq;acc:nm_178832]	Squared	Divided	1	148058	99628.4	1.4861
	60s ribosomal protein l12. [swissprot;acc:p30050]		Subtracted	0	3686.65	4639.46	952.81
	calsyntenin-1 precursor. [swissprot;acc:o94985]			1	71062.4	95488.9	24426.5
	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Measured		0	3053.31	2799.81	253.5
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared	Divided		21165.1	38499.2	1.81899
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Ranked			14476.2	17069.5	1.17914
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured		1	2234.68	2978.53	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted			55.1026	67.5701	1.22626

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.