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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 77072 in total

Rank	Network Comparison Type	description	Filtered	Value Type	Interaction Map	red	network_comparison	green
13	Subtracted	adenomatous polyposis coli like. [refseq;acc:nm_005883]	0	Rooted	Low confidence	27.8758	11.4764	39.3522
		adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	Measured	High confidence	1363	1316	47
		beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	1	Rooted		80.4705	21.0555	101.526
		cab2. [refseq;acc:nm_033419]	0	Rooted		0	13.1909	13.1909
		dystrophin. [swissprot;acc:p11532]		Ranked		10232.5	7822.3	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	20324.1	5578	14746.1
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1		High confidence	266.856	69.377	336.233
		homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	1	Measured	Low confidence	15464.1	2108.6	17572.7
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	Squared	High confidence	1.73869	19294.2	19295.9
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1	Squared		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]		Rooted	Low confidence	186.878	17.179	204.057
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		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]	0	Squared		38389.3	11170.5	49559.8
		sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	0	Measured		2961.07	992.25	3953.32
14	Divided	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1	Squared		7744.68	1.56161	4959.41
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	Squared	High confidence	1.73869	11098	19295.9
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Rooted	Low confidence	9.20014	6.52932	60.0707
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		Measured	High confidence	130.512	20.0687	6.50325
		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1	Ranked	High confidence	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]	1	Rooted	Low confidence	39.2489	1.33864	52.5401
		dystrophin. [swissprot;acc:p11532]	0	Ranked	High confidence	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]		Measured	Low confidence	0.00001	5900000	59
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Squared	Low confidence	174.646	219.346	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	0.00001	424264	4.24264
		ptd016 protein. [refseq;acc:nm_016125]		Ranked	Low confidence	18050	1.60673	11234
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	Measured	High confidence	398.5	3.21581	1281.5
				Squared		37.5863	10.3414	388.696
				Rooted		19.9625	1.79326	35.798
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]		Measured	Low confidence	1972.65	1.51983	2998.1
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Ranked		37.9984	1.30207	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		286.396	47.92	238.476
		apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	Measured	High confidence	10817.1	1308	12125.1
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Ranked	Low confidence	13730.5	5473.5	8257
		block 23. [sptrembl;acc:q8nhw5]		Squared	Low confidence	38133.9	11090.7	49224.6
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		Rooted	High confidence	39.9124	13.0404	52.9528
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1	Ranked	High confidence	266.863	69.328	336.191
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Squared	Low confidence	122475	37292	159767
		homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]		Measured	Low confidence	15464.1	2108.6	17572.7
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		Squared	High confidence	219048	89286	129762
		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]		Measured		21591.5	6313	27904.5
		protein cgi-147. [swissprot;acc:q9y3e5]	0	Squared		75129.2	19048.8	94178
		protein kinase, lysine deficient 3. [refseq;acc:nm_020922]		Rooted	Low confidence	10.6742	11.0842	21.7584
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]		Measured	Low confidence	17235.5	940.4	16295.1
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	Rooted	High confidence	80.4705	21.0555	101.526
		ubiquitin protein ligase. [refseq;acc:nm_130466]	0	Ranked	High confidence	7523	7816.2	15339.2
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	1	Rooted	Low confidence	186.878	17.179	204.057
15	Divided	adenomatous polyposis coli like. [refseq;acc:nm_005883]	0	Ranked		12074.1	1.5892	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		39.8493	1.32836	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/