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	Filtered	green	Interaction Map	red	network_comparison

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Showing element 551 to 600 of 66312 in total

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