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 6158 to 6207 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
770	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Ranked	Subtracted	59	49	10
	transforming protein rhoa (h12). [swissprot;acc:p06749]	Rooted		63.5181	67.7402	4.2221
	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	Divided	5874.74	6533.34	1.11211
771	40s ribosomal protein s19. [swissprot;acc:p39019]	Rooted		55.6817	59.3786	1.06639
	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]	Measured		5874.74	6533.34	1.11211
	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	Squared	Subtracted	24509.4	28571.6	4062.2
	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	Ranked	Divided	210.946	221.225	1.04873
	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292]	Squared		24418	28453.7	1.16528
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Ranked	Subtracted	59	49	10
	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	Measured		5622.89	6260.02	637.13
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Rooted		50.5979	46.392	4.2059
772	60s ribosomal protein l31. [swissprot;acc:p12947]		Divided	55.6817	59.3786	1.06639
	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Ranked		210.946	221.225	1.04873
	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]	Squared		24418	28453.7	1.16528
	homolog of yeast maf1. [refseq;acc:nm_032272]		Subtracted	26029.5	30074.5	4045
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured		3494.31	4129.6	635.29
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Ranked		59	49	10
	sec13-related protein. [swissprot;acc:p55735]	Measured	Divided	5874.76	6533.36	1.11211
	syntaxin 7. [swissprot;acc:o15400]	Rooted	Subtracted	61.5022	65.7076	4.2054
773	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]			50.2583	46.057	4.2013
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Ranked		59	49	10
	coactosin-like protein. [swissprot;acc:q14019]	Squared	Divided	24418	28453.7	1.16528
	jm1 protein. [refseq;acc:nm_014008]	Measured	Subtracted	5794.8	6427.79	632.99
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Rooted	Divided	127.967	120.003	1.06637
	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Ranked		210.946	221.225	1.04873
	tumor differentially expressed protein 2. [refseq;acc:nm_178865]	Squared	Subtracted	26029.5	30074.5	4045
	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	Divided	5874.74	6533.34	1.11211
774	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	Rooted		65.3248	69.648	1.06618
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]		Subtracted	78.3617	82.5529	4.1912
	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Ranked		221.716	231.501	9.785
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]		Divided	225.996	215.535	1.04854
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	Measured	Subtracted	5384.41	6012.82	628.41
	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]	Squared		26029.5	30074.5	4045
	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]		Divided	24418	28453.7	1.16528
	yeast sec31p homolog. [refseq;acc:nm_014933]	Measured		5874.76	6533.36	1.11211
775	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	Rooted	Subtracted	50.7935	46.6042	4.1893
	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]		Divided	62.2385	58.38	1.06609
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Ranked		226.003	215.541	1.04854
	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	Measured	Subtracted	5384.41	6012.82	628.41
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Squared	Divided	24418	28453.7	1.16528
	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]		Subtracted	26029.5	30074.5	4045
	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Ranked		221.676	231.453	9.777
	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]	Measured	Divided	5874.74	6533.33	1.11211
776	40s ribosomal protein s13. [swissprot;acc:q02546]	Squared		21976	25607.9	1.16527
	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	Measured	Subtracted	5317.78	5944.25	626.47
	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]	Squared		26029.5	30074.5	4045
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Ranked	Divided	225.996	215.535	1.04854
	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	Measured		5874.76	6533.36	1.11211
	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	Ranked	Subtracted	221.965	212.404	9.561
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Rooted		59.7414	63.909	4.1676

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.