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

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Showing element 1844 to 1893 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]	1287	Divided	1	218.368	213.22	1.02414
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	285		0	10686	9925.58	1.07661
	297	Subtracted				760.42
	496		1	235.18	250.419	15.239
	576	Divided				1.0648
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	488	Subtracted	0	11999.1	12041.7	42.6
	493	Divided				1.00355
	2599	Subtracted	1	224.891	225.195	0.304
	2621	Divided				1.00135
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	37		0	3859	2582	1.49458
	183	Subtracted				1277
	2408	Divided	1	194.407	193.706	1.00362
	2439	Subtracted				0.701
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	87	Divided	0	5677.89	4547.43	1.24859
	217	Subtracted				1130.46
	3025	Divided	1	0.00001	0.00001	1
		Subtracted		0	0	0
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	82	Divided	0	7706.5	6058	1.27212
	148	Subtracted				1648.5
	699		1	220.438	209.118	11.32
	700	Divided				1.05413
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	316		0	10768.5	11444	1.06273
	327	Subtracted				675.5
	1125	Divided	1	204.404	210.022	1.02748
	1133	Subtracted				5.618
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	222	Divided		112	126	1.125
	544	Subtracted				14
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	132			229.406	196.695	32.711
	177	Divided				1.1663
	194	Subtracted	0	13573.3	14801.2	1227.9
	263	Divided				1.09046
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	455	Subtracted		12189.6	12378.3	188.7
	462	Divided				1.01548
	1879	Subtracted	1	210.592	208.355	2.237
	1881	Divided				1.01074
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	74	Subtracted	0	14548.5	11915.2	2633.3
	101	Divided				1.221
	1304	Subtracted	1	218.509	213.648	4.861
	1329	Divided				1.02275
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	82	Subtracted	0	14466.8	12031.7	2435.1
	109	Divided				1.20239
	1302	Subtracted	1	218.509	213.648	4.861
	1326	Divided				1.02275
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	248	Subtracted		243.583	267.527	23.944
	339	Divided				1.0983
	395		0	10195.5	9856.7	1.03437
	407	Subtracted				338.8
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	1008		1	222.364	215.535	6.829
	1029	Divided				1.03168
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	116	Subtracted	0	11123.4	13000.1	1876.7

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.