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 5708 to 5757 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
714	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]	Ranked	Subtracted	224.434	235.583	11.149
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]		Divided	223.121	211.685	1.05402
	vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864]	Measured	Subtracted	5873.77	6532.44	658.67
		Squared	Divided	25904.2	30273.7	1.16868
	vinculin (metavinculin). [swissprot;acc:p18206]	Rooted	Subtracted	62.9163	67.3603	4.444
715	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]			50.1766	45.7369	4.4397
	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	Ranked	Divided	223.121	211.685	1.05402
	cellular modulator of immune recognition. [refseq;acc:nm_145021]	Squared	Subtracted	25114	29386	4272
	dendritic cell protein. [refseq;acc:nm_006360]	Measured	Divided	6593.17	7364.55	1.117
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	Rooted		61.0097	65.3071	1.07044
	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]	Ranked	Subtracted	224.434	235.583	11.149
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Measured		5874.74	6533.34	658.6
		Squared	Divided	25911.5	30281.9	1.16867
716	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Rooted	Subtracted	50.1636	45.7275	4.4361
	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]	Measured		5874.74	6533.34	658.6
		Squared	Divided	25911.5	30281.9	1.16867
	cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	Ranked	Subtracted	224.434	235.583	11.149
	cpz gene product. [refseq;acc:nm_003652]		Divided	223.121	211.685	1.05402
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Rooted		61.0098	65.3071	1.07044
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	Measured		6593.17	7364.55	1.117
	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]	Squared	Subtracted	25114	29386	4272
717	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]	Ranked		224.434	235.583	11.149
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]		Divided	223.121	211.685	1.05402
	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	Measured		6593.17	7364.55	1.117
	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]	Squared	Subtracted	25114	29386	4272
	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Rooted	Divided	61.0111	65.3081	1.07043
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]		Subtracted	50.1635	45.7274	4.4361
	sec13-related protein. [swissprot;acc:p55735]	Measured		5874.76	6533.36	658.6
		Squared	Divided	25911.7	30282.1	1.16867
718	60s ribosomal protein l7. [swissprot;acc:p18124]	Rooted	Subtracted	52.6483	48.2135	4.4348
	cpz gene product. [refseq;acc:nm_003652]	Measured	Divided	6593.17	7364.55	1.117
	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	Squared	Subtracted	26421.1	30691.2	4270.1
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	Rooted	Divided	60.7498	65.0218	1.07032
	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]	Ranked	Subtracted	224.434	235.583	11.149
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]		Divided	223.121	211.685	1.05402
	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4]	Measured	Subtracted	5874.74	6533.34	658.6
		Squared	Divided	25911.5	30281.9	1.16867
719	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Measured		6593.17	7364.55	1.117
	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	Ranked	Subtracted	230.516	241.641	11.125
	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	Squared		29990.9	34251.1	4260.2
	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	Ranked	Divided	247.769	235.074	1.054
	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	Rooted		60.7498	65.0218	1.07032
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]		Subtracted	50.4595	46.0411	4.4184
	yeast sec31p homolog. [refseq;acc:nm_014933]	Measured		5874.76	6533.36	658.6
		Squared	Divided	25911.7	30282.1	1.16867
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	Ranked		231.92	244.435	1.05396
	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	Measured	Subtracted	5874.76	6533.36	658.6
	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Rooted		50.4595	46.0412	4.4183
	jm1 protein. [refseq;acc:nm_014008]		Divided	61.5849	65.9155	1.07032
	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	Squared	Subtracted	24633.6	28893.6	4260

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.