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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Gene	Network Comparison Type	red	Value Type	green	Rank	Interaction Map	description	Filtered	network_comparison

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Showing element 1425 to 1474 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

red	green	Rank	description	network_comparison
5438.6	5783.11	1888	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]	1.06335
		1890	nag14 protein. [refseq;acc:nm_022143]
5438.66	5893.87	1255	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	1.0837
		1257	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318]
5438.68	5783.2	1889	testis-specific bromodomain protein. [refseq;acc:nm_001726]	1.06335
5439.56	5911.24	1195	similar to trna synthetase class ii. [refseq;acc:nm_152268]	1.08671
5444.6	5783.95	1919	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	1.06233
5448.35	5777.35	1958	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333]	1.06039
		1959	splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081]
		1960	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
		1961	splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368]
5449.48	5921.77	1199	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	1.08667
5450.9	5869.07	1443	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	1.07672
		1444	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
5454.62	5637.88	2442	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	1.0336
5456.57	5816.14	1799	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	1.0659
5457.14	5899.85	1313	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	1.08112
5458.12	5830.76	1719	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	1.06827
		1720	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]
		1721	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
		1722	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]
		1723	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
		1724	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
5460.49	5954.62	1105	synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	1.09049
5462.88	5958.12	1102	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9]	1.09066
5464.9	5940.16	1193	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	1.08697
5466	5865.33	1542	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	1.07306
		1543	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
		1544	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]
5470.44	5949.49	1168	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	1.08757
		1169	zinc finger protein 207. [swissprot;acc:o43670]
5473.09	5887.45	1468	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	1.07571
		1469	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
		1470	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
5475.44	5127.66	1728	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	1.06782
5475.74	5800.97	1978	uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725]	1.05939
		1979	26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
		1981	inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968]
		1982	uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727]
		1983	myosin vi. [swissprot;acc:q9um54]
5480.24	6222.04	560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	1.13536
		561	transforming protein rhoc (h9). [swissprot;acc:p08134]
		562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
		563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
		564	transforming protein rhoa (h12). [swissprot;acc:p06749]
5488.7	5131.89	1655	40s ribosomal protein s26. [swissprot;acc:p02383]	1.06953
		1656	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]
		1657	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
		1659	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
5489.18	5972.09	1158	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	1.08797

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.