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 551 to 600 of 66312 in total

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Rank	description	Value Type	Network Comparison Type	red	Interaction Map	green	network_comparison
35	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Rooted	Divided	40.2812	High confidence	24.3679	1.65304
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	Subtracted	82347.8	Low confidence	61881.5	20466.3
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured		23693.7	High confidence	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared		106226		192141	85915
	necdin. [swissprot;acc:q99608]		Divided	82347.8	Low confidence	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		260.532	High confidence	204.309	1.27519
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Rooted		54.8296	Low confidence	63.2347	1.15329
	rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872]	Measured	Subtracted	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]	Ranked	Divided	297.273		258.59	1.14959
36	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	Measured	Subtracted	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]	Ranked	Divided	260.532	High confidence	204.309	1.27519
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Rooted		55.7086	Low confidence	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]	Squared	Subtracted	227160	High confidence	146079	81081
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked		267.376	Low confidence	240.78	26.596
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured	Divided	1836.76	High confidence	907.741	2.02344
		Rooted		40.2805		24.369	1.65294
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured	Subtracted	23693.7		18263	5430.7
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared		82347.8	Low confidence	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]			106226	High confidence	192141	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	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]	Measured	Divided	6462.09	Low confidence	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]	Rooted	Subtracted	51.3588		60.737	9.3782
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Divided	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	266.716	High confidence	333.165	66.449
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Measured	Divided	1836.76		907.763	2.02339
		Rooted		40.2805		24.3691	1.65293
	jun dimerization protein. [refseq;acc:nm_130469]	Measured		6462.09	Low confidence	7593.77	1.17513
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Ranked	Subtracted	234.802		260.98	26.178
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured		23693.7	High confidence	18263	5430.7
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Squared		82347.8	Low confidence	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]	Rooted	Subtracted	26.0288	High confidence	43.1914	17.1626
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared	Divided	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]	Rooted	Subtracted	66.5831	Low confidence	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]	Rooted	Divided	51.7058		59.166	1.14428
	trs85 homolog. [swissprot;acc:q9y2l5]	Squared	Subtracted	227160	High confidence	146079	81081
38	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	Rooted	Divided	51.7058	Low confidence	59.166	1.14428
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	Subtracted	13195.9		11486.4	1709.5
	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Ranked	Divided	247.202		282.937	1.14456
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]		Subtracted	266.933	High confidence	333.281	66.348
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Measured	Divided	1836.76		907.774	2.02337
		Rooted		40.2804		24.3692	1.65292
	jun dimerization protein. [refseq;acc:nm_130469]		Subtracted	66.5831	Low confidence	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.