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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Gene	Rank	description	Network Comparison Type	Value Type	Interaction Map	green	Filtered	network_comparison	red

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

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.