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 2401 to 2450 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
601	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	Squared	34129.6	40434.5	1.18473
	symplekin. [swissprot;acc:q92797]	Measured	15213.4	13418.1	1.1338
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Ranked	206.274	218.792	1.06069
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Rooted	138.032	127.651	1.08132
602	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	Measured	4864.66	5514.87	1.13366
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Rooted	138.032	127.651	1.08132
	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	Ranked	206.274	218.792	1.06069
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Squared	19129.8	22652.9	1.18417
603	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Measured	4864.66	5514.87	1.13366
	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	Ranked	225.829	212.945	1.0605
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Squared	34071.5	40336.5	1.18388
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Rooted	60.0742	64.9418	1.08103
604	60s ribosomal protein l15. [swissprot;acc:p39030]	Ranked	217.862	230.978	1.0602
	alpha-nac protein. [sptrembl;acc:q9h009]	Squared	34069.4	40333	1.18385
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Rooted	60.0742	64.9418	1.08103
	vinculin (metavinculin). [swissprot;acc:p18206]	Measured	5958.23	6743.37	1.13177
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Ranked	247.47	233.441	1.0601
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Measured	6143.52	6950.75	1.1314
	sedlin. [swissprot;acc:o14582]	Rooted	116.061	125.434	1.08076
	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Squared	34068.1	40330.8	1.18383
606	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	Measured	6148.94	6955.76	1.13121
	di-ras2. [refseq;acc:nm_017594]	Squared	34068	40330.7	1.18383
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Ranked	247.47	233.441	1.0601
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Rooted	116.061	125.434	1.08076
607	bet3 homolog. [swissprot;acc:o43617]
	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	Squared	26583.8	31468.6	1.18375
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Ranked	247.47	233.441	1.0601
	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Measured	14976.4	13246.6	1.13058
608	histone h2b. [refseq;acc:nm_175055]	Ranked	247.47	233.441	1.0601
	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	Squared	24560.6	29071.1	1.18365
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Measured	4510.61	5098.74	1.13039
	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	Rooted	59.6517	64.4642	1.08068
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Measured	3886.62	3438.82	1.13022
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Ranked	247.47	233.441	1.0601
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Rooted	62.9281	67.99	1.08044
	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	Squared	12276.9	14526	1.1832
610	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Rooted	136.706	126.565	1.08012
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Ranked	247.47	233.441	1.0601
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Measured	8430.03	9518.11	1.12907
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Squared	12347.6	14594.8	1.18199
611	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]		23487.1	27726.3	1.18049
	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	Measured	5148.71	5811.74	1.12878
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Ranked	247.47	233.441	1.0601
	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Rooted	51.0091	55.0909	1.08002
612	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	Measured	3975.77	4485.05	1.1281
	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	Rooted	57.1949	61.7633	1.07987
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Ranked	247.47	233.441	1.0601
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Squared	18595.6	21936.3	1.17965
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Ranked	247.47	233.441	1.0601
	n-myc proto-oncogene protein. [swissprot;acc:p04198]	Rooted	57.1971	61.7626	1.07982

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.