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

Results: HTML CSV LaTeX

Showing element 24626 to 24675 of 29840 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
2577	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	Ranked	Subtracted	213.422	213.75	0.328
	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]		Divided	192.625	192.922	1.00154
	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]	Rooted		71.5023	72.1247	1.0087
	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]		Subtracted	55.7376	55.2091	0.5285
	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Measured		6380.6	6476.18	95.58
	translin. [swissprot;acc:q15631]		Divided	4979.44	5071.53	1.01849
	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	Squared	Subtracted	28127.2	28939	811.8
2578	40s ribosomal protein s26. [swissprot;acc:p02383]		Divided	23172.9	22157.6	1.04582
	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	Measured	Subtracted	6380.61	6476.19	95.58
	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]	Ranked	Divided	213.422	213.75	1.00154
			Subtracted			0.328
	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]	Rooted	Divided	71.5023	72.1247	1.0087
	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	Squared	Subtracted	28128.8	28940.3	811.5
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	Measured	Divided	4979.44	5071.53	1.01849
	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	Rooted	Subtracted	70.9263	71.4475	0.5212
2579	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]			80.3593	79.843	0.5163
	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	Squared	Divided	23172.9	22157.6	1.04582
	nitrilase 1. [refseq;acc:nm_005600]	Ranked		213.422	213.75	1.00154
			Subtracted			0.328
	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]	Measured	Divided	4979.44	5071.53	1.01849
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]		Subtracted	6380.6	6476.18	95.58
	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	Rooted	Divided	71.504	72.1264	1.0087
	trap/mediator complex component trap25. [refseq;acc:nm_080651]	Squared	Subtracted	28128.8	28940.3	811.5
2580	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]		Divided	23172.9	22157.6	1.04582
	disrupter of silencing 10. [refseq;acc:nm_020368]	Rooted		71.5023	72.1247	1.0087
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Measured		4331.39	4252.8	1.01848
	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	Rooted	Subtracted	67.3258	66.8099	0.5159
	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]	Squared		28128.8	28940.3	811.5
	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	Measured		6380.61	6476.19	95.58
	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]	Ranked	Divided	213.422	213.75	1.00154
			Subtracted			0.328
2581	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	Measured	Divided	4570.81	4654.97	1.01841
	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	Ranked		213.428	213.756	1.00154
			Subtracted			0.328
	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Squared		28128.8	28940.3	811.5
	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]	Measured		6380.61	6476.19	95.58
	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	Rooted		62.9549	63.4703	0.5154
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	Squared	Divided	23172.9	22157.6	1.04582
	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	Rooted		71.5025	72.1249	1.0087
2582	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	Squared	Subtracted	28128.8	28940.3	811.5
	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]		Divided	23107	22137	1.04382
	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	Rooted	Subtracted	62.9549	63.4703	0.5154
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Measured	Divided	3899.28	3829.53	1.01821
	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]	Ranked		213.422	213.75	1.00154
			Subtracted			0.328
	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	Rooted	Divided	71.5034	72.1258	1.0087
	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	Measured	Subtracted	6380.84	6476.41	95.57
2583	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	Rooted	Divided	59.5216	60.0368	1.00866
	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	Ranked		213.415	213.743	1.00154
			Subtracted			0.328

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.