Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

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Showing element 401 to 450 of 77072 in total

Rank	Network Comparison Type	description	Filtered	Value Type	Interaction Map	network_comparison	red	green
13	Subtracted	adenomatous polyposis coli like. [refseq;acc:nm_005883]	0	Rooted	Low confidence	11.4764	27.8758	39.3522
		adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	Measured	High confidence	1316	1363	47
		beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	1	Rooted		21.0555	80.4705	101.526
		cab2. [refseq;acc:nm_033419]	0	Rooted		13.1909	0	13.1909
		dystrophin. [swissprot;acc:p11532]		Ranked		7822.3	10232.5	18054.8
		fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]			Low confidence	5578	20324.1	14746.1
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1		High confidence	69.377	266.856	336.233
		homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	1	Measured	Low confidence	2108.6	15464.1	17572.7
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	Squared	High confidence	19294.2	1.73869	19295.9
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1	Squared		89286	219048	129762
		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		Measured		6313	21591.5	27904.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Rooted	Low confidence	17.179	186.878	204.057
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		Ranked		52.684	255.046	202.362
		rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783]		Squared		53522	281799	228277
		similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	0	Squared		11170.5	38389.3	49559.8
		sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	0	Measured		992.25	2961.07	3953.32
14	Divided	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1	Squared		1.56161	7744.68	4959.41
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	Squared	High confidence	11098	1.73869	19295.9
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Rooted	Low confidence	6.52932	9.20014	60.0707
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		Measured	High confidence	20.0687	130.512	6.50325
		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1	Ranked	High confidence	1.32952	56.6768	75.3531
		cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	1	Rooted	Low confidence	1.33864	39.2489	52.5401
		dystrophin. [swissprot;acc:p11532]	0	Ranked	High confidence	1.76446	10232.5	18054.8
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]		Measured	Low confidence	5900000	0.00001	59
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Squared	Low confidence	219.346	174.646	0.796213
		phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]		Rooted	High confidence	424264	0.00001	4.24264
		ptd016 protein. [refseq;acc:nm_016125]		Ranked	Low confidence	1.60673	18050	11234
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	Measured	High confidence	3.21581	398.5	1281.5
				Squared		10.3414	37.5863	388.696
				Rooted		1.79326	19.9625	35.798
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]		Measured	Low confidence	1.51983	1972.65	2998.1
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Ranked		1.30207	37.9984	29.1831
	Subtracted	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]		Ranked		47.92	286.396	238.476
		apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	Measured	High confidence	1308	10817.1	12125.1
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Ranked	Low confidence	5473.5	13730.5	8257
		block 23. [sptrembl;acc:q8nhw5]		Squared	Low confidence	11090.7	38133.9	49224.6
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		Rooted	High confidence	13.0404	39.9124	52.9528
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1	Ranked	High confidence	69.328	266.863	336.191
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Squared	Low confidence	37292	122475	159767
		homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]		Measured	Low confidence	2108.6	15464.1	17572.7
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Squared	High confidence	89286	219048	129762
		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]		Measured		6313	21591.5	27904.5
		protein cgi-147. [swissprot;acc:q9y3e5]	0	Squared		19048.8	75129.2	94178
		protein kinase, lysine deficient 3. [refseq;acc:nm_020922]		Rooted	Low confidence	11.0842	10.6742	21.7584
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]		Measured	Low confidence	940.4	17235.5	16295.1
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	Rooted	High confidence	21.0555	80.4705	101.526
		ubiquitin protein ligase. [refseq;acc:nm_130466]	0	Ranked	High confidence	7816.2	7523	15339.2
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	1	Rooted	Low confidence	17.179	186.878	204.057
15	Divided	adenomatous polyposis coli like. [refseq;acc:nm_005883]	0	Ranked		1.5892	12074.1	7597.61
15	Divided	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	1	Rooted		1.32836	39.8493	52.9343

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.

- http://analysis.yellowcouch.org/