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 network_comparison green Filtered

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Showing element 401 to 450 of 77072 in total

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