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	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 551 to 600 of 66312 in total

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Rank	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
35	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Divided	Rooted	High confidence	40.2812	24.3679	1.65304
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		Measured	High confidence	23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Squared		106226	192141	85915
	necdin. [swissprot;acc:q99608]	Divided		Low confidence	82347.8	61881.5	1.33073
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]		Ranked	High confidence	260.532	204.309	1.27519
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]		Rooted	Low confidence	54.8296	63.2347	1.15329
	rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872]	Subtracted	Measured		23239.9	21503.3	1736.6
	sperm associated antigen 7. [refseq;acc:nm_004890]		Rooted		132.137	122.736	9.401
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	Ranked		297.273	258.59	1.14959
36	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	Subtracted	Measured		23239.9	21503.3	1736.6
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Divided	Ranked	High confidence	260.532	204.309	1.27519
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		Rooted	Low confidence	55.7086	64.217	1.15273
	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]	Subtracted	Squared	High confidence	227160	146079	81081
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		Ranked	Low confidence	267.376	240.78	26.596
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Divided	Measured	High confidence	1836.76	907.741	2.02344
			Rooted		40.2805	24.369	1.65294
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Subtracted	Measured		23693.7	18263	5430.7
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided					1.33073
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]			High confidence	106226	192141	1.80879
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Subtracted	Ranked		320.927	254.434	66.493
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		Rooted		26.0288	43.1914	17.1626
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Divided	Measured	Low confidence	6462.09	7593.77	1.17513
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Subtracted	Rooted		51.3588	60.737	9.3782
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	Ranked		296.837	258.33	1.14906
37	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]				250.244	217.843	1.14874
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Subtracted		High confidence	266.716	333.165	66.449
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Divided	Measured		1836.76	907.763	2.02339
			Rooted		40.2805	24.3691	1.65293
	jun dimerization protein. [refseq;acc:nm_130469]		Measured	Low confidence	6462.09	7593.77	1.17513
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	Ranked		234.802	260.98	26.178
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		Measured	High confidence	23693.7	18263	5430.7
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		Squared	Low confidence	82347.8	61881.5	20466.3
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Divided					1.33073
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Subtracted	Rooted	High confidence	26.0288	43.1914	17.1626
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Divided	Squared		106226	192141	1.80879
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		Ranked		322	253	1.27273
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Subtracted	Rooted	Low confidence	66.5831	75.4064	8.8233
	rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783]		Measured		23239.9	21503.3	1736.6
	testis-specific protein tex28. [swissprot;acc:o15482]	Divided	Rooted		51.7058	59.166	1.14428
	trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	Squared	High confidence	227160	146079	81081
38	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	Divided	Rooted	Low confidence	51.7058	59.166	1.14428
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	Measured		13195.9	11486.4	1709.5
	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Divided	Ranked		247.202	282.937	1.14456
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Subtracted		High confidence	266.933	333.281	66.348
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Divided	Measured		1836.76	907.774	2.02337
			Rooted		40.2804	24.3692	1.65292
	jun dimerization protein. [refseq;acc:nm_130469]	Subtracted		Low confidence	66.5831	75.4064	8.8233
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		Ranked		234.802	260.98	26.178

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.