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	red	Interaction Map	Filtered	green	network_comparison

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Showing element 501 to 550 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	Interaction Map	green	network_comparison
32	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Ranked	Subtracted	267.142	High confidence	336.074	68.932
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	Divided	1834.73		895.893	2.04793
	implantation-associated protein. [refseq;acc:nm_032121]		Subtracted	3278	Low confidence	5058.5	1780.5
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	Divided	82347.8		61881.5	1.33073
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Measured	Subtracted	23693.7	High confidence	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	Divided	145.551	Low confidence	168.796	1.1597
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured		36360.3		43368.8	1.19275
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Squared	Subtracted	106226	High confidence	192141	85915
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	Divided	273.188	Low confidence	232.49	1.17505
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]		Subtracted	247.768		219.841	27.927
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]		Divided	187.462	High confidence	243.673	1.29985
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Rooted	Subtracted	38.4152	Low confidence	49.1529	10.7377
33	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Ranked		228.147		200.55	27.597
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared		77316.3		56522.1	20794.2
	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	Ranked	Divided	210.241		246.125	1.17068
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]		Subtracted	267.144	High confidence	336.073	68.929
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	Divided	1835.3		896.972	2.04611
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared		82347.8	Low confidence	61881.5	1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Measured	Subtracted	23693.7	High confidence	18263	5430.7
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared		106226		192141	85915
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted		25.6987		43.561	17.8623
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]		Divided	26.0288		43.1914	1.65937
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]			76.5734	Low confidence	88.6244	1.15738
	septin 6. [swissprot;acc:q14141]	Measured	Subtracted	13005.8		14773.7	1767.9
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Ranked	Divided	188.688	High confidence	242.742	1.28647
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared		9924.76		25146.6	2.53372
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Rooted	Subtracted	38.5678	Low confidence	49.2633	10.6955
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Measured	Divided	36360.3		43368.8	1.19275
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared		9924.76	High confidence	25146.6	2.53372
	bcl2-related ovarian killer. [refseq;acc:nm_032515]	Rooted	Subtracted	50.6099	Low confidence	61.2591	10.6492
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Measured		5492.04		7251	1758.96
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted		140.508	High confidence	122.878	17.63
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Ranked		227.371	Low confidence	200.532	26.839
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]			267.144	High confidence	336.073	68.929
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	Divided	1836.71		907.546	2.02382
		Rooted		40.2812		24.3678	1.65305
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	82347.8	Low confidence	61881.5	20466.3
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]		Divided				1.33073
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured	Subtracted	23693.7	High confidence	18263	5430.7
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Squared		106226		192141	85915
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	Divided	5339.5	Low confidence	6352.4	1.1897
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked		155.56		133.876	1.16197
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted		49.0544		56.755	1.15698
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Ranked		189.07	High confidence	242.453	1.28235
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Squared		106226		192141	1.80879
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Rooted	Subtracted	140.508		122.878	17.63
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked		267.448	Low confidence	240.822	26.626
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Measured	Divided	33111.4		39358.1	1.18866
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked	Subtracted	267.636	High confidence	335.359	67.723
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Measured	Divided	1836.71		907.564	2.02378

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.