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 Value Type Filtered green Network Comparison Type red Interaction Map network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	description	Value Type	Filtered	green	Network Comparison Type	red	Interaction Map	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	0	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
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Measured	1	32028.5	Subtracted	40899	Low confidence	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
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0	1.87479	Divided	0.00001	Low confidence	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	1	543.5	Divided	2399.5		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
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0	0.00001	Divided	364	High confidence	36400000
				0.00001	Divided	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	Subtracted	232467	Low confidence	72283
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	1	24	Divided	10	High confidence	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	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured		28492		21185	Low confidence	7307
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	0	15915		4294	High confidence	11621
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared	1	475119		333556	Low confidence	141563
	cab2. [refseq;acc:nm_033419]	Measured	0	174	Divided	0.00001	High confidence	17400000
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Measured	1	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
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured		33356.5		41482.5	High confidence	8126
	hbs1-like. [refseq;acc:nm_006620]	Ranked		322		215		107
	histone h4. [swissprot;acc:p02304]	Squared	0	345123		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
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	1	330	Divided	223	Low confidence	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/