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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 77072 in total

Rank	description	Network Comparison Type	Interaction Map	Value Type	Filtered	red	network_comparison	green
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Divided	High confidence	Ranked	0	5210.5	1.77804	9264.5
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Subtracted	Low confidence	Measured	1	15464.1	2108.6	17572.7
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Divided	Low confidence	Measured	1	1927.68	1.5351	2959.19
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	High confidence	Squared	0	1.73869	19294.2	19295.9
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]			Squared	1	219048	89286	129762
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]			Measured		21591.5	6313	27904.5
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	Low confidence	Ranked		37.9984	1.30207	29.1831
		Subtracted	Low confidence	Rooted		186.878	17.179	204.057
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	High confidence	Ranked		288.754	1.3585	212.554
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	Low confidence	Ranked		255.046	52.684	202.362
	rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783]			Squared		281799	53522	228277
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]			Squared	0	38389.3	11170.5	49559.8
	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	Divided		Ranked		7435.56	1.63963	12191.6
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Subtracted		Measured		2961.07	992.25	3953.32
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Divided		Squared		0.00219609	219.609	0.00001
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Divided		Rooted		17.0721	7.72053	2.21126
14	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		Ranked	1	286.396	47.92	238.476
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Subtracted	High confidence	Measured	0	10817.1	1308	12125.1
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Divided	Low confidence	Squared	1	7744.68	1.56161	4959.41
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		High confidence	Squared	0	1.73869	11098	19295.9
			Low confidence	Rooted		9.20014	6.52932	60.0707
		Subtracted		Ranked		13730.5	5473.5	8257
	block 23. [sptrembl;acc:q8nhw5]	Subtracted		Squared		38133.9	11090.7	49224.6
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	High confidence	Measured		130.512	20.0687	6.50325
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		High confidence	Ranked	1	56.6768	1.32952	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]		Low confidence	Rooted	1	39.2489	1.33864	52.5401
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Subtracted	High confidence	Rooted	0	39.9124	13.0404	52.9528
	dystrophin. [swissprot;acc:p11532]	Divided	High confidence	Ranked		10232.5	1.76446	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]	Divided	Low confidence	Measured		0.00001	5900000	59
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	High confidence	Ranked	1	266.863	69.328	336.191
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	Squared		122475	37292	159767
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]		Low confidence	Measured		15464.1	2108.6	17572.7
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		High confidence	Squared		219048	89286	129762
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	Low confidence	Squared	0	174.646	219.346	0.796213
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Subtracted	High confidence	Measured	1	21591.5	6313	27904.5
	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		Rooted	0	0.00001	424264	4.24264
	protein cgi-147. [swissprot;acc:q9y3e5]	Subtracted		Squared		75129.2	19048.8	94178
	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Subtracted	Low confidence	Rooted		10.6742	11.0842	21.7584
	ptd016 protein. [refseq;acc:nm_016125]	Divided	Low confidence	Ranked		18050	1.60673	11234
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]		High confidence	Measured	1	398.5	3.21581	1281.5
				Squared		37.5863	10.3414	388.696
				Rooted		19.9625	1.79326	35.798
	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	Subtracted	Low confidence	Measured	0	17235.5	940.4	16295.1
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	High confidence	Rooted	1	80.4705	21.0555	101.526
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Divided	Low confidence	Measured	1	1972.65	1.51983	2998.1
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Subtracted	High confidence	Ranked	0	7523	7816.2	15339.2
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Divided	Low confidence	Ranked	1	37.9984	1.30207	29.1831
		Subtracted		Rooted	1	186.878	17.179	204.057
15	adenomatous polyposis coli like. [refseq;acc:nm_005883]	Divided		Ranked	0	12074.1	1.5892	7597.61
15	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Subtracted	High confidence	Rooted	1	80.4705	21.0555	101.526

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/