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

Results: HTML CSV LaTeX

Showing element 1980 to 2029 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
124	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Measured	Divided	0	3248.95	2399.76	1.35386
	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]	Squared			2.70982	1.44	1.88182
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Rooted	Subtracted		56.49	52.4119	4.0781
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Squared	Divided	1	192779	126095	1.52884
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Ranked		0	11520.7	13680.4	1.18746
125	aquaporin 5. [swissprot;acc:p55064]	Squared	Subtracted	1	71388.5	96035.2	24646.7
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Ranked		0	12314.9	10489.3	1825.6
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Rooted			13.7413	17.8164	4.0751
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Measured			3691.15	3952.59	261.44
	high-mobility group 20a. [refseq;acc:nm_018200]	Ranked	Divided	1	208.588	171.778	1.21429
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Measured	Subtracted		12471.7	14561.7	2090
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		Divided		24255.7	18168.9	1.33501
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Squared	Subtracted	0	1495.1	509.542	985.558
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]		Divided		10.3503	19.2071	1.8557
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Ranked			22038	18578	1.18624
	pp3111 protein. [refseq;acc:nm_022156]	Rooted			28.0891	23.0217	1.22011
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Measured			1095.42	812.166	1.34876
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Squared		1	189976	124480	1.52616
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Ranked	Subtracted		285.684	252.234	33.45
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Rooted	Divided		54.8203	67.934	1.23921
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]		Subtracted		35.6294	49.8119	14.1825
126	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			71387.4	96033.4	24646
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	Divided		94	114	1.21277
	calcyphosine. [swissprot;acc:q13938]	Measured		0	472.524	635.875	1.3457
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]			1	24250	18164.9	1.33499
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Ranked	Subtracted	0	12314.9	10489.3	1825.6
	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	Squared	Divided		118.204	219.216	1.85456
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]		Subtracted		3339.18	2360.97	978.21
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Rooted	Divided		21.3244	25.9172	1.21538
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Ranked	Subtracted	1	285.684	252.234	33.45
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted			60.9353	75.094	14.1587
	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]		Divided		60.9342	75.1387	1.23311
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]		Subtracted	0	11.0328	6.96286	4.06994
	pp3111 protein. [refseq;acc:nm_022156]	Measured			789	530	259
	rad50-interacting protein 1. [refseq;acc:nm_021930]			1	450.5	2394.5	1944
	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]	Ranked	Divided	0	9722.71	11493.8	1.18216
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared		1	189976	124480	1.52616
127	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Measured	Subtracted	0	2017.91	1759.22	258.69
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Rooted			25.8457	21.7945	4.0512
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Ranked			11732	13530.6	1798.6
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]			1	285.684	252.234	33.45
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared	Divided		88432.6	58423.3	1.51365
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Rooted	Subtracted		153.191	166.771	13.58
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Squared		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

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.