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

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Showing element 401 to 450 of 77072 in total

Rank	Value Type	description	Network Comparison Type	Interaction Map	red	green	network_comparison	Filtered
13	Squared	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Divided	Low confidence	395912	242799	1.63062	1
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		High confidence	37.5863	388.696	10.3414	1
		dok-like protein. [refseq;acc:nm_024872]			0.289941	0.00001	28994.1	0
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted		1.73869	19295.9	19294.2	0
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]			219048	129762	89286	1
		rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783]		Low confidence	281799	228277	53522	1
		similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]			38389.3	49559.8	11170.5	0
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Divided		0.00219609	0.00001	219.609	0
	Rooted	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]	Divided		39.2301	52.5277	1.33896	1
		adenomatous polyposis coli like. [refseq;acc:nm_005883]	Subtracted		27.8758	39.3522	11.4764	0
		beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		High confidence	80.4705	101.526	21.0555	1
		cab2. [refseq;acc:nm_033419]			0	13.1909	13.1909	0
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided		19.9625	35.798	1.79326	1
		dok-like protein. [refseq;acc:nm_024872]	Divided		5.91608	0.00001	591608	0
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Low confidence	186.878	204.057	17.179	1
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Divided	Low confidence	17.0721	2.21126	7.72053	0
14	Measured	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Subtracted	High confidence	10817.1	12125.1	1308
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	High confidence	130.512	6.50325	20.0687
		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]	Divided	Low confidence	0.00001	59	5900000
		homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Subtracted	Low confidence	15464.1	17572.7	2108.6	1
		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Subtracted	High confidence	21591.5	27904.5	6313
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	High confidence	398.5	1281.5	3.21581
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	Subtracted	Low confidence	17235.5	16295.1	940.4	0
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Divided		1972.65	2998.1	1.51983	1
	Ranked	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]	Subtracted		286.396	238.476	47.92	1
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted		13730.5	8257	5473.5	0
		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Divided	High confidence	56.6768	75.3531	1.32952	1
		dystrophin. [swissprot;acc:p11532]	Divided		10232.5	18054.8	1.76446	0
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted		266.863	336.191	69.328	1
		ptd016 protein. [refseq;acc:nm_016125]	Divided	Low confidence	18050	11234	1.60673	0
		ubiquitin protein ligase. [refseq;acc:nm_130466]	Subtracted	High confidence	7523	15339.2	7816.2	0
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Divided	Low confidence	37.9984	29.1831	1.30207	1
	Squared	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		Low confidence	7744.68	4959.41	1.56161	1
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		High confidence	1.73869	19295.9	11098	0
		block 23. [sptrembl;acc:q8nhw5]	Subtracted	Low confidence	38133.9	49224.6	11090.7	0
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	122475	159767	37292	1
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		High confidence	219048	129762	89286	1
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	Low confidence	174.646	0.796213	219.346	0
		protein cgi-147. [swissprot;acc:q9y3e5]	Subtracted	High confidence	75129.2	94178	19048.8	0
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	High confidence	37.5863	388.696	10.3414	1
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Low confidence	9.20014	60.0707	6.52932	0
		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]		Low confidence	39.2489	52.5401	1.33864	1
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Subtracted	High confidence	39.9124	52.9528	13.0404	0
		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]	Divided	High confidence	0.00001	4.24264	424264
		protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Subtracted	Low confidence	10.6742	21.7584	11.0842
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	High confidence	19.9625	35.798	1.79326	1
		spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	High confidence	80.4705	101.526	21.0555
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Low confidence	186.878	204.057	17.179
15	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]			15464.1	17572.7	2108.6
15	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Divided		485.286	2740.13	5.64642	0

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/