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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	description	Network Comparison Type	Interaction Map	Value Type	Filtered	red	green	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Divided	High confidence	Ranked	0	4294	15915	3.70633
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted		Measured		85	6410	6325
				Rooted		9.20014	60.0707	50.8706
			Low confidence	Measured		85	6410	6325
			Low confidence	Rooted		9.20014	60.0707	50.8706
	cab2. [refseq;acc:nm_033419]	Divided	High confidence	Squared		0.00001	7.16592	716592
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Divided	Low confidence	Ranked	1	16	32	2
		Subtracted		Measured		40899	32028.5	8870.5
				Squared		395912	242799	153113
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		High confidence	Ranked		215	322	107
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Low confidence	Squared	0	0.00001	1.87479	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]			Measured	1	2399.5	543.5	4.4149
				Squared		1362.75	69.9153	19.4914
				Rooted		48.9847	23.3131	2.10117
		Subtracted		Ranked		223	330	107
				Rooted		48.9847	23.3131	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]		High confidence	Measured		41482.5	33356.5	8126
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided		Measured	0	364	0.00001	36400000
				Rooted		19.0788		1907880
			Low confidence	Measured		364		36400000
			Low confidence	Rooted		19.0788		1907880
		Subtracted	High confidence	Ranked		8906	21883	12977
		Subtracted	Low confidence			8906	21883	12977
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	Low confidence			5865	14977	2.55362
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	High confidence	Squared		232467	160184	72283
		Subtracted	Low confidence	Squared		232467	160184	72283
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	High confidence	Ranked	1	10	24	2.4
		Subtracted		Squared		468498	322755	145743
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		Measured		450.5	2394.5	5.31521
				Squared		48.0356	1357.07	28.2513
				Rooted		21.225	48.9336	2.30547
		Subtracted		Rooted		21.225	48.9336	27.7086
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Low confidence	Measured		21185	28492	7307
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		High confidence	Ranked	0	4294	15915	11621
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Low confidence	Squared	1	333556	475119	141563
	cab2. [refseq;acc:nm_033419]	Divided	High confidence	Measured	0	0.00001	174	17400000
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Low confidence	Measured	1	2399.5	543.5	4.4149
				Squared		1362.75	69.9153	19.4914
				Rooted		48.9847	23.3131	2.10117
		Subtracted		Ranked		223	330	107
				Rooted		48.9847	23.3131	25.6716
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		High confidence	Measured		41482.5	33356.5	8126
	hbs1-like. [refseq;acc:nm_006620]			Ranked		215	322	107
	histone h4. [swissprot;acc:p02304]			Squared	0	273623	345123	71500
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Low confidence	Measured		0.00001	89	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]	Subtracted	High confidence	Measured		85	6410	6325
		Subtracted	High confidence	Rooted		9.20014	60.0707	50.8706
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	Low confidence	Ranked	1	223	330	1.47982

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/