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	Interaction Map	Network Comparison Type	network_comparison	Filtered	red	green

Results: HTML CSV LaTeX

Showing element 851 to 900 of 19268 in total

Value Type  : Measured

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