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	Value Type	description	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	Value Type	description	red	green	network_comparison
601	Measured	symplekin. [swissprot;acc:q92797]	15213.4	13418.1	1.1338
	Ranked	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	206.274	218.792	1.06069
	Squared	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	34129.6	40434.5	1.18473
	Rooted	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	138.032	127.651	1.08132
602	Measured	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	4864.66	5514.87	1.13366
	Ranked	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	206.274	218.792	1.06069
	Squared	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	19129.8	22652.9	1.18417
	Rooted	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	138.032	127.651	1.08132
603	Measured	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	4864.66	5514.87	1.13366
	Ranked	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	225.829	212.945	1.0605
	Squared	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	34071.5	40336.5	1.18388
	Rooted	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	60.0742	64.9418	1.08103
604	Measured	vinculin (metavinculin). [swissprot;acc:p18206]	5958.23	6743.37	1.13177
	Ranked	60s ribosomal protein l15. [swissprot;acc:p39030]	217.862	230.978	1.0602
	Squared	alpha-nac protein. [sptrembl;acc:q9h009]	34069.4	40333	1.18385
	Rooted	step ii splicing factor slu7. [refseq;acc:nm_006425]	60.0742	64.9418	1.08103
605	Measured	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	6143.52	6950.75	1.1314
	Ranked	histone h2b.c (h2b/c). [swissprot;acc:q99880]	247.47	233.441	1.0601
	Squared	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	34068.1	40330.8	1.18383
	Rooted	sedlin. [swissprot;acc:o14582]	116.061	125.434	1.08076
606	Measured	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]	6148.94	6955.76	1.13121
	Ranked	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	247.47	233.441	1.0601
	Squared	di-ras2. [refseq;acc:nm_017594]	34068	40330.7	1.18383
	Rooted	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	116.061	125.434	1.08076
607	Measured	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	14976.4	13246.6	1.13058
	Ranked	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	247.47	233.441	1.0601
	Squared	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	26583.8	31468.6	1.18375
	Rooted	bet3 homolog. [swissprot;acc:o43617]	116.061	125.434	1.08076
608	Measured	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]	4510.61	5098.74	1.13039
	Ranked	histone h2b. [refseq;acc:nm_175055]	247.47	233.441	1.0601
	Squared	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	24560.6	29071.1	1.18365
	Rooted	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	59.6517	64.4642	1.08068
609	Measured	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	3886.62	3438.82	1.13022
	Ranked	histone h2b.s (h2b/s). [swissprot;acc:p57053]	247.47	233.441	1.0601
	Squared	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	12276.9	14526	1.1832
	Rooted	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	62.9281	67.99	1.08044
610	Measured	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	8430.03	9518.11	1.12907
	Ranked	histone h2b.d (h2b/d). [swissprot;acc:q99877]	247.47	233.441	1.0601
	Squared	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	12347.6	14594.8	1.18199
	Rooted	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	136.706	126.565	1.08012
611	Measured	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	5148.71	5811.74	1.12878
	Ranked	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	247.47	233.441	1.0601
	Squared	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
	Rooted	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	51.0091	55.0909	1.08002
612	Measured	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	3975.77	4485.05	1.1281
	Ranked	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	247.47	233.441	1.0601
	Squared	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	18595.6	21936.3	1.17965
	Rooted	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	57.1949	61.7633	1.07987
613	Measured	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	3975.77	4485.05	1.1281
	Ranked	histone h2b.e (h2b/e). [swissprot;acc:q99879]	247.47	233.441	1.0601

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.