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 2375 to 2424 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Ranked	223.282	210.136	1.06256
	transforming protein n-ras. [swissprot;acc:p01111]	Rooted	108.65	100.35	1.08271
595	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	Squared	34129.7	40434.8	1.18474
	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	Rooted	51.2427	55.468	1.08246
	histone h2b. [refseq;acc:nm_175055]	Measured	3946.32	4475.47	1.13409
	vav proto-oncogene. [swissprot;acc:p15498]	Ranked	212.2	199.849	1.0618
596	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	Squared	34129.6	40434.5	1.18473
	cbf1 interacting corepressor. [refseq;acc:nm_004882]	Rooted	60.0587	65.0057	1.08237
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Measured	3946.32	4475.47	1.13409
	vav-3 protein. [swissprot;acc:q9ukw4]	Ranked	212.253	199.908	1.06175
597	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Squared	34129.4	40434.2	1.18473
	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	Rooted	60.0587	65.0057	1.08237
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Measured	3946.32	4475.47	1.13409
	vav-2 protein. [swissprot;acc:p52735]	Ranked	212.526	200.212	1.0615
598	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	Squared	34129.6	40434.5	1.18473
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Measured	3946.32	4475.47	1.13409
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Rooted	61.2527	66.2644	1.08182
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Ranked	248.463	234.095	1.06138
599	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	Squared	34129.6	40434.5	1.18473
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Rooted	138.375	127.926	1.08168
	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	Ranked	248.463	234.095	1.06138
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Measured	3946.32	4475.47	1.13409
600	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	Squared	34129.6	40434.5	1.18473
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Measured	3946.32	4475.47	1.13409
	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Ranked	248.463	234.095	1.06138
	trs85 homolog. [swissprot;acc:q9y2l5]	Rooted	138.375	127.926	1.08168
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

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.