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 4808 to 4857 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
301	kappa b-ras 1. [refseq;acc:nm_020345]	Squared	Divided	0	1558.15	1297.17	1.20119
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Rooted		1	203.673	182.638	1.11517
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked	Subtracted		88.2482	110.265	22.0168
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]			0	16321	15577	744
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Rooted			9.00325	7.33715	1.6661
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Measured		1	4446.72	5553.79	1107.07
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared	Divided		28896.2	36767	1.27238
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]		Subtracted	0	948.513	872.867	75.646
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Ranked	Divided		12783	13698	1.07158
302	60s ribosomal protein l18a. [swissprot;acc:q02543]	Squared	Subtracted		9310.69	9385.52	74.83
	60s ribosomal protein l26. [swissprot;acc:q02877]	Ranked	Divided	1	242.326	267.008	1.10185
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Squared		0	61.898	74.2593	1.1997
	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]		Subtracted	1	51527.6	43689.1	7838.5
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Rooted	Divided		203.673	182.638	1.11517
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]		Subtracted	0	27.5028	29.1579	1.6551
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Ranked	Divided		7386.71	6895.44	1.07125
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]		Subtracted	1	88.2482	110.265	22.0168
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Rooted			66.1046	74.0964	7.9918
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Measured	Divided	0	135.294	149.371	1.10405
	lats homolog 1. [refseq;acc:nm_004690]	Rooted			10.2412	9.54479	1.07296
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Ranked	Subtracted		16321	15577	744
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Measured	Divided	1	5894.75	7073.65	1.19999
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]		Subtracted		6704.44	7811.45	1107.01
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]			0	729.216	642.343	86.873
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	Squared	Divided	1	28896.2	36767	1.27238
303	60s ribosomal protein l35. [swissprot;acc:p42766]	Ranked			242.333	266.999	1.10179
	crk-like protein. [swissprot;acc:p46109]	Squared			28896.2	36767	1.27238
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Rooted			203.673	182.638	1.11517
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Ranked		0	11431.4	12244.1	1.07109
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Squared			1487.24	1783.26	1.19904
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Ranked	Subtracted		16321	15577	744
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]			1	88.2482	110.265	22.0168
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Rooted		0	27.5028	29.1579	1.6551
	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]	Squared		1	51527.6	43689.1	7838.5
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]			0	76.8994	4.57302	72.3264
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Rooted		1	62.9007	70.8854	7.9847
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Measured	Divided		22268.8	18560.4	1.1998
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]			0	952.488	863.886	1.10256
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Rooted			10.2412	9.54479	1.07296
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Measured	Subtracted	1	4723.53	5828.46	1104.93
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]			0	331.61	417.983	86.373
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked	Divided	1	242.339	266.986	1.1017
	40s ribosomal protein s28. [swissprot;acc:p25112]	Squared		0	1054.58	879.603	1.19893
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Rooted	Subtracted		25.2821	26.9306	1.6485
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Squared			76.8994	4.57302	72.3264
	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]			1	51527.6	43689.1	7838.5
	cytohesin 4. [swissprot;acc:q9uia0]	Rooted	Divided		203.673	182.638	1.11517
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked	Subtracted	0	16321	15577	744
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]			1	88.2482	110.265	22.0168
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Measured			5221.28	6314.35	1093.07

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.