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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	Filtered	description	Value Type	green	Network Comparison Type	red	Interaction Map	network_comparison
1	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	15915	Divided	4294	High confidence	3.70633
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Measured	6410	Subtracted	85	High confidence	6325
			Measured	6410		85	Low confidence	6325
			Rooted	60.0707		9.20014	High confidence	50.8706
			Rooted	60.0707		9.20014	Low confidence	50.8706
		cab2. [refseq;acc:nm_033419]	Squared	7.16592	Divided	0.00001	High confidence	716592
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	1.87479		0.00001	Low confidence	187479
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	0.00001		364	High confidence	36400000
			Measured	0.00001		364	Low confidence	36400000
			Ranked	21883	Subtracted	8906	High confidence	12977
			Ranked	21883	Subtracted	8906	Low confidence	12977
			Rooted	0.00001	Divided	19.0788	High confidence	1907880
			Rooted	0.00001		19.0788	Low confidence	1907880
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	14977		5865	Low confidence	2.55362
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	160184	Subtracted	232467	High confidence	72283
			Squared	160184		232467	Low confidence	72283
	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Measured	32028.5		40899		8870.5
			Ranked	32	Divided	16		2
			Squared	242799	Subtracted	395912		153113
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	322	Subtracted	215	High confidence	107
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	543.5	Divided	2399.5	Low confidence	4.4149
			Ranked	330	Subtracted	223		107
			Squared	69.9153	Divided	1362.75		19.4914
			Rooted	23.3131	Divided	48.9847		2.10117
			Rooted	23.3131	Subtracted	48.9847		25.6716
		mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured	33356.5	Subtracted	41482.5	High confidence	8126
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	24	Divided	10		2.4
			Squared	322755	Subtracted	468498		145743
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	2394.5	Divided	450.5		5.31521
			Squared	1357.07		48.0356		28.2513
			Rooted	48.9336		21.225		2.30547
			Rooted	48.9336	Subtracted	21.225		27.7086
2	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	15915	Subtracted	4294		11621
		cab2. [refseq;acc:nm_033419]	Measured	174	Divided	0.00001		17400000
		histone h4. [swissprot;acc:p02304]	Squared	345123	Subtracted	273623		71500
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	89	Divided	0.00001	Low confidence	8900000
			Rooted	9.43398				943398
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	1.87479				187479
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured	6410	Subtracted	85	High confidence	6325
			Rooted	60.0707	Subtracted	9.20014	High confidence	50.8706
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	21883	Divided	8906	Low confidence	2.45711
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	14977	Divided	5865	High confidence	2.55362
			Rooted	7.61577	Subtracted	29.3087	Low confidence	21.6929
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked	20617		9607		11010
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	19621.3		23818.1		4196.8
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	0.00001	Divided	5.61325	High confidence	561325
			Rooted	0.00001	Divided	12.4097	High confidence	1240970
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Squared	386144	Subtracted	414704	Low confidence	28560
	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	28492		21185		7307
	1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared	475119		333556		141563

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/