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 173 to 222 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
44	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	1931.34	1057.39	1.82652
	Ranked	fos-related antigen 2. [swissprot;acc:p15408]	204.641	161.046	1.2707
	Squared	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	139741	78454.6	1.78117
	Rooted	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	40.5691	25.4263	1.59556
45	Measured		1926.69	1056.02	1.82448
	Ranked	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	204.641	161.051	1.27066
	Squared	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	129597	73157.5	1.77148
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	40.081	25.1546	1.59339
46	Measured	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	779.167	1390.33	1.78438
	Ranked	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	204.642	161.068	1.27053
	Squared	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	129597	73157.5	1.77148
	Rooted	deltex 2. [refseq;acc:nm_020892]	27.634	43.9629	1.5909
47	Measured	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	779.167	1390.33	1.78438
	Ranked	gbp protein isoform a. [refseq;acc:nm_017870]	325.586	256.492	1.26938
	Squared	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	98517.9	56927.2	1.73059
	Rooted	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	27.7078	44.017	1.58861
48	Measured	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	779.167	1390.33	1.78438
	Ranked	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	65.4586	83.0461	1.26868
	Squared	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	6300.2	10703.5	1.69891
	Rooted	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	27.7254	44.0299	1.58807
49	Measured	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	779.167	1390.33	1.78438
	Ranked	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	133	105	1.26667
	Squared	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	28994.2	17134.8	1.69212
	Rooted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	27.7254	44.0299	1.58807
50	Measured	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	779.167	1390.33	1.78438
	Ranked	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	133	105	1.26667
	Squared	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	28994.2	17134.8	1.69212
	Rooted	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	27.7254	44.0299	1.58807
51	Measured	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	779.167	1390.33	1.78438
	Ranked	spermatogenesis associated 6. [refseq;acc:nm_019073]	133	105	1.26667
	Squared	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	28994.2	17134.8	1.69212
	Rooted	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	27.7254	44.0299	1.58807
52	Measured	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	779.167	1390.33	1.78438
	Ranked	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	133	105	1.26667
	Squared	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	28994.2	17134.8	1.69212
	Rooted	neuralized-like. [refseq;acc:nm_004210]	27.9107	44.1656	1.58239
53	Measured	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	779.167	1390.33	1.78438
	Ranked	transcription factor jun-b. [swissprot;acc:p17275]	201.144	158.868	1.26611
	Squared	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	28994.2	17134.8	1.69212
	Rooted	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	30.8986	46.4619	1.50369
54	Measured	deltex 2. [refseq;acc:nm_020892]	1618.84	2651.88	1.63814
	Ranked	transcription factor jun-d. [swissprot;acc:p17535]	200.941	158.941	1.26425
	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	219048	129762	1.68808
	Rooted	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	40.0958	58.7986	1.46645
55	Measured	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1629.21	2662.12	1.63399
	Ranked	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	320.927	254.434	1.26134
	Squared	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	219048	129762	1.68808
	Rooted	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	41.6734	28.9323	1.44038
56	Measured	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	1631.67	2664.55	1.63302
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	266.856	336.233	1.25998

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.