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

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Showing element 3908 to 3957 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
245	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted	Divided	0	22.6521	25.1534	1.11042
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Ranked			11867.6	13019	1.09702
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Rooted	Subtracted	1	27.9136	37.2872	9.3736
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared			40315.7	49716.4	9400.7
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Rooted		0	10.6611	13.034	2.3729
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Measured	Divided	1	4251.65	5212.33	1.22595
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Squared	Subtracted	0	219.839	59.1928	160.646
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Measured	Divided		1225.09	1079.36	1.13502
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Ranked	Subtracted		10551.6	11573.5	1021.9
	methyltransferase like 2. [refseq;acc:nm_018396]	Measured		1	13241.4	11864	1377.4
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted	Divided		146.94	167.046	1.13683
	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]	Squared		0	10596.4	8278.87	1.27993
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Ranked		1	226.109	202.333	1.11751
246	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		Subtracted		243.583	267.528	23.945
	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	Rooted		0	28.8531	26.484	2.3691
	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Measured		1	13241.4	11864	1377.4
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Squared		0	57.8417	218.049	160.207
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Rooted		1	27.9136	37.2872	9.3736
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Ranked	Divided		237.312	212.363	1.11748
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Measured	Subtracted	0	150.673	279.24	128.567
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Squared	Divided	1	8875.01	6768.05	1.31131
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]			0	7273.2	9308.93	1.27989
	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]		Subtracted	1	54726.7	45358.5	9368.2
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Measured	Divided		4252.66	5213.05	1.22583
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Ranked		0	10551.6	11573.7	1.09687
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Measured			1225.09	1079.36	1.13502
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Rooted			12.8935	14.3151	1.11026
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]			1	146.94	167.046	1.13683
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Ranked	Subtracted	0	10551.6	11573.5	1021.9
247	60s ribosomal protein l12. [swissprot;acc:p30050]			1	243.583	267.527	23.944
	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Squared	Divided	0	20324.3	15893.2	1.2788
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]		Subtracted		323.856	482.631	158.775
	espin. [refseq;acc:nm_031475]	Ranked			10551.6	11573.4	1021.8
	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Measured		1	13241.4	11864	1377.4
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Squared	Divided		8875.01	6768.05	1.31131
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Measured		0	1225.09	1079.36	1.13502
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Ranked			10551.6	11573.7	1.09687
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Rooted	Subtracted		9.1258	11.4849	2.3591
	neurocalcin delta. [swissprot;acc:p29554]		Divided		12.8769	11.6055	1.10955
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]		Subtracted	1	27.9136	37.2872	9.3736
	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	Squared			33982.3	43159.1	9176.8
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Rooted	Divided		47.3621	53.8355	1.13668
	rna-binding protein. [refseq;acc:nm_019027]	Ranked			237.302	212.41	1.11719
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Measured	Subtracted	0	271.484	142.981	128.503
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]		Divided	1	6416.68	7865.15	1.22574
248	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]		Subtracted	0	2323.8	2452.23	128.43
	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Ranked	Divided	1	237.302	212.41	1.11719
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		Subtracted		243.583	267.527	23.944
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Rooted	Divided	0	30.7397	27.7265	1.10868
	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]		Subtracted		19.7165	17.3602	2.3563

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.