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

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Showing element 1560 to 1609 of 6456 in total

Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

description	Rank	Network Comparison Type	red	network_comparison	green
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	1525	Subtracted	213.267	3.756	209.511
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	367		218.827	19.58	238.407
	394	Divided		1.08948
diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	809	Subtracted	233.298	9.273	242.571
	868	Divided		1.03975
diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]	1114	Subtracted	227.274	5.767	233.041
	1202	Divided		1.02537
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]	700	Subtracted	220.438	11.32	209.118
	701	Divided		1.05413
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	707	Subtracted		11.32
	708	Divided		1.05413
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]	705	Subtracted		11.32
	706	Divided		1.05413
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]	709	Subtracted		11.32
	710	Divided		1.05413
disrupter of silencing 10. [refseq;acc:nm_020368]	1905		191.411	1.01034	193.39
	1981	Subtracted		1.979
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	641		244.842	12.265	232.577
	724	Divided		1.05274
dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]	2039	Subtracted	218.79	1.809	216.981
	2060	Divided		1.00834
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	744	Subtracted	225.996	10.461	215.535
	776	Divided		1.04854
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]	1255	Subtracted	218.368	5.148	213.22
	1287	Divided		1.02414
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	496	Subtracted	235.18	15.239	250.419
	576	Divided		1.0648
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	2599	Subtracted	224.891	0.304	225.195
	2621	Divided		1.00135
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2408		194.407	1.00362	193.706
	2439	Subtracted		0.701
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	3025	Divided	0.00001	1	0.00001
		Subtracted	0	0	0
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	699		220.438	11.32	209.118
	700	Divided		1.05413
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	1125		204.404	1.02748	210.022
	1133	Subtracted		5.618
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	222	Divided	112	1.125	126
	544	Subtracted		14
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	132		229.406	32.711	196.695
	177	Divided		1.1663
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	1879	Subtracted	210.592	2.237	208.355
	1881	Divided		1.01074
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	1304	Subtracted	218.509	4.861	213.648
	1329	Divided		1.02275
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	1302	Subtracted		4.861
	1326	Divided		1.02275
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	248	Subtracted	243.583	23.944	267.527
	339	Divided		1.0983
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	Subtracted	222.364	6.829	215.535

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.