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 green Value Type Network Comparison Type red Interaction Map network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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