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 2160 to 2209 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
135	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Rooted	Subtracted	1	49.2923	62.3969	13.1046
136	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Squared		0	6747.71	5878.56	869.15
	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted	Divided	1	41.8357	50.6469	1.21061
	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Squared	Subtracted		71030.1	95434.8	24404.7
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured			12787.6	10880.5	1907.1
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Ranked	Divided	0	12335.3	10506.8	1.17403
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]			1	350	290	1.2069
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Rooted		0	23.9877	20.1222	1.1921
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Ranked	Subtracted	1	263.215	231.407	31.808
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Measured		0	903.767	1152.06	248.293
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]		Divided	1	3620.77	4763.34	1.31556
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Ranked	Subtracted	0	12759.4	11028.8	1730.6
		Rooted			14.7363	18.7165	3.9802
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	Divided		978.105	1746.18	1.78527
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Measured			1526.38	1150.51	1.3267
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared		1	81888.8	56306.5	1.45434
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Rooted	Subtracted		49.2923	62.3969	13.1046
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Measured	Divided		3620.77	4763.34	1.31556
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared			81606.8	56215.8	1.45167
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Ranked		0	12328.5	10501	1.17403
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted	Subtracted		13.7191	17.6786	3.9595
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked		1	263.191	231.394	31.797
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured			12786.6	10879.9	1906.7
	heat shock factor binding protein 1. [swissprot;acc:o75506]		Divided	0	1631.18	1233.41	1.3225
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Squared	Subtracted		26171.8	27038.8	867
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Ranked			16853	15123	1730
		Squared	Divided		0.417515	0.742249	1.77778
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted		1	54.9787	66.2416	1.20486
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked			350	290	1.2069
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Measured	Subtracted	0	7520.78	7276.12	244.66
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted	Divided		18.9056	15.8624	1.19185
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	Subtracted	1	69549	92953.5	23404.5
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted			49.2925	62.397	13.1045
138	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Measured		0	1663.73	1906.28	242.55
	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked		1	174.667	205.556	30.889
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Rooted		0	18.4959	14.5738	3.9221
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared		1	70739	93908.8	23169.8
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Rooted	Divided	0	22.775	19.1245	1.19088
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Squared	Subtracted		25552.2	26410.4	858.2
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	Divided	1	2755.15	2094.3	1.31555
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Ranked		0	12384.7	10549.4	1.17397
	musashi 1. [refseq;acc:nm_002442]	Rooted		1	54.9787	66.2416	1.20486
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared			468498	322755	1.45156
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Ranked			194.372	234.204	1.20493
	serpin b11. [swissprot;acc:q96p15]		Subtracted	0	16853	15123	1730
		Squared	Divided		0.417515	0.742249	1.77778
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Measured	Subtracted	1	15182.5	13277.9	1904.6
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]		Divided	0	204.382	154.804	1.32026
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	Subtracted	1	49.293	62.3973	13.1043
139	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]			0	5.11118	9.0312	3.92002

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.