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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Gene	Value Type	Rank	description	Network Comparison Type	Interaction Map	Filtered	red	network_comparison	green

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Showing element 851 to 900 of 19268 in total

Value Type  : Measured

Rank	description	Network Comparison Type	Interaction Map	Filtered	red	network_comparison	green
107	60s ribosomal protein l7. [swissprot;acc:p18124]	Subtracted	High confidence	0	1915.27	290.8	2206.07
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Divided			326.677	1.4467	472.605
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Subtracted		1	14229.2	2551.5	16780.7
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Divided	Low confidence	0	160	1.42539	112.25
	tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881]			1	11371	1.09746	12479.2
	zinc finger protein 415. [refseq;acc:nm_018355]	Subtracted		0	2352.12	382.97	1969.15
108	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Divided	High confidence		292	1.44178	421
	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Subtracted	Low confidence	1	3035.43	882.45	3917.88
	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]	Divided	High confidence		4366.44	1.35116	5899.76
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Subtracted		0	482.426	290.131	192.295
	nanos (fragment). [sptrembl;acc:q8wy41]	Divided	Low confidence		338.761	1.41306	478.69
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Subtracted	High confidence	1	14021.4	2498.4	11523
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Divided	Low confidence		10499	1.09685	11515.8
	zinc finger protein 10 (zinc finger protein kox1) (fragment). [swissprot;acc:p21506]	Subtracted		0	2352.16	382.97	1969.19
109	44050 protein. [refseq;acc:nm_178832]		High confidence	1	17385.9	2496.7	14889.2
	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]		Low confidence		3126.88	870.14	3997.02
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Divided	High confidence	0	100	1.44	144
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]			1	4366.44	1.35116	5899.76
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Subtracted		0	934.726	288.164	1222.89
	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	Divided	Low confidence	1	7354.65	1.0966	8065.08
	zinc finger protein 225. [swissprot;acc:q9uk10]	Subtracted		0	2352.16	382.97	1969.19
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Divided			385	1.41039	543
110	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Subtracted	High confidence		528.5	288	816.5
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Divided	Low confidence		967.877	1.38222	1337.82
	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]			1	7206.99	1.09572	7896.81
	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	Subtracted			10452.8	868	11320.8
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]		High confidence		17385.9	2496.7	14889.2
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Divided			4366.44	1.35116	5899.76
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]			0	1833	1.43863	2637
	zinc finger protein 256 (bone marrow zinc finger 3) (bmzf-3). [swissprot;acc:q9y2p7]	Subtracted	Low confidence		2352.16	382.97	1969.19
111	brain protein 44. [swissprot;acc:o95563]			1	10392.1	867.6	11259.7
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided			11285.3	1.0937	10318.5
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]		High confidence		4366.44	1.35116	5899.76
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]			0	2965.5	1.43747	2063
			Low confidence		1763.83	1.37838	1279.64
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Subtracted	High confidence		10247.8	287.2	10535
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]			1	12365.2	2459.7	14824.9
	zinc finger protein 214 (bwscr2 associated zinc-finger protein 1) (baz 1). [swissprot;acc:q9ul59]		Low confidence	0	2352.16	382.97	1969.19
112	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]		High confidence	1	11757.8	2405.69	9352.11
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Divided	Low confidence		11285.3	1.0937	10318.5
	lats homolog 1. [refseq;acc:nm_004690]		High confidence	0	160	1.42539	112.25
	monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375]	Subtracted	Low confidence	1	10351.8	859	11210.8
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]		High confidence	0	1095.42	283.254	812.166
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Divided	Low confidence		1392.08	1.37602	1011.67
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]		High confidence	1	4366.44	1.35116	5899.76
	zinc finger protein 165 (ld65). [swissprot;acc:p49910]	Subtracted	Low confidence	0	2352.16	382.97	1969.19
113	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		High confidence	1	4800.81	2331.9	7132.71
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Divided			4366.44	1.35116	5899.76
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		Low confidence		11285.3	1.0937	10318.5
	monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985]	Subtracted			10348.5	858.2	11206.7

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.