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	Interaction Map	Filtered	red	green	network_comparison

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Showing element 6762 to 6811 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
423	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Rooted	Divided	0	6.9282	7.14143	1.03078
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]		Subtracted	1	60.0148	65.6429	5.6281
	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	Measured	Divided		5207.03	6010.1	1.15423
	oligophrenin 1. [swissprot;acc:o60890]	Ranked	Subtracted		238.704	255.68	16.976
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Rooted		0	23.2671	22.7187	0.5484
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Ranked	Divided	1	240.287	260.193	1.08284
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Squared			36735.7	44689.6	1.21652
424	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted			50.4703	45.9373	1.09868
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Ranked	Subtracted	0	11276.1	11582.7	306.6
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]		Divided		9562.48	9298.93	1.02834
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Rooted	Subtracted		10.603	10.0581	0.5449
	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	Ranked	Divided	1	240.287	260.193	1.08284
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Measured		0	3967.18	4091.59	1.03136
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Squared	Subtracted	1	32183.5	37955.7	5772.2
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Measured			6739.63	7644.59	904.96
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Rooted			51.9812	57.5858	5.6046
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Measured		0	81.504	60.8613	20.6427
	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	Squared	Divided	1	20259.5	24635.7	1.21601
	mstp028 protein. [refseq;acc:nm_031954]			0	105962	110835	1.04599
	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Measured		1	5207.78	6010.45	1.15413
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Ranked	Subtracted		251.83	234.951	16.879
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Rooted	Divided	0	48.9929	50.4997	1.03076
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Subtracted		8.15919	4.74982	3.40937
425	40s ribosomal protein s20. [swissprot;acc:p17075]	Rooted	Divided	1	50.0161	45.5318	1.09849
	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Ranked	Subtracted		212.547	229.411	16.864
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Measured			6739.7	7644.6	904.9
	max protein. [swissprot;acc:p25912]	Ranked	Divided		227.828	210.561	1.082
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Measured	Subtracted	0	34.6667	54.6667	20
	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	Squared	Divided	1	20258.6	24634.7	1.21601
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Rooted	Subtracted		48.1584	53.7378	5.5794
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Squared		0	8.27669	4.90793	3.36876
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Measured	Divided		2070.81	2134.56	1.03079
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]			1	3729.02	4301.58	1.15354
	scribble. [refseq;acc:nm_015356]	Ranked		0	12370.5	12719	1.02817
		Squared			4169.68	3987.55	1.04567
	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]		Subtracted	1	28408.7	34148.5	5739.8
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Rooted		0	17.5059	16.9709	0.535
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]		Divided		133.419	129.687	1.02878
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Ranked	Subtracted		16416.1	16721.6	305.5
426	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared			26.2121	22.8932	3.3189
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]		Divided		14907.5	15522.7	1.04127
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Ranked			9412.67	9676.67	1.02805
	dendritic cell protein. [refseq;acc:nm_006360]	Squared	Subtracted	1	33104	38818.5	5714.5
	dynactin 4. [refseq;acc:nm_032486]	Ranked	Divided		233.142	252.253	1.08197
	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	Measured	Subtracted		6739.81	7644.62	904.81
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Rooted			66.0815	71.6562	5.5747
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]		Divided	0	22.1458	22.7768	1.02849
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]			1	55.1073	60.5285	1.09838
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Measured			5942.49	6853.15	1.15325
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Ranked	Subtracted		212.547	229.411	16.864

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.