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 Filtered Value Type Interaction Map network_comparison Network Comparison Type green red

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	description	Filtered	Value Type	Interaction Map	network_comparison	Network Comparison Type	green	red
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	Ranked	High confidence	3.70633	Divided	15915	4294
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Measured	High confidence	6325	Subtracted	6410	85
			Measured	Low confidence	6325		6410	85
			Rooted	High confidence	50.8706		60.0707	9.20014
			Rooted	Low confidence	50.8706		60.0707	9.20014
	cab2. [refseq;acc:nm_033419]		Squared	High confidence	716592	Divided	7.16592	0.00001
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	Measured	Low confidence	8870.5	Subtracted	32028.5	40899
			Ranked		2	Divided	32	16
			Squared		153113	Subtracted	242799	395912
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Ranked	High confidence	107	Subtracted	322	215
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	Squared	Low confidence	187479	Divided	1.87479	0.00001
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	Measured		4.4149	Divided	543.5	2399.5
			Ranked		107	Subtracted	330	223
			Squared		19.4914	Divided	69.9153	1362.75
			Rooted		2.10117	Divided	23.3131	48.9847
			Rooted		25.6716	Subtracted	23.3131	48.9847
	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	High confidence	8126	Subtracted	33356.5	41482.5
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0		High confidence	36400000	Divided	0.00001	364
				Low confidence	36400000	Divided	0.00001	364
			Ranked	High confidence	12977	Subtracted	21883	8906
			Ranked	Low confidence	12977	Subtracted	21883	8906
			Rooted	High confidence	1907880	Divided	0.00001	19.0788
			Rooted	Low confidence	1907880		0.00001	19.0788
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Ranked	Low confidence	2.55362		14977	5865
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Squared	High confidence	72283	Subtracted	160184	232467
			Squared	Low confidence	72283	Subtracted	160184	232467
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	Ranked	High confidence	2.4	Divided	24	10
			Squared		145743	Subtracted	322755	468498
	rad50-interacting protein 1. [refseq;acc:nm_021930]		Measured		5.31521	Divided	2394.5	450.5
			Squared		28.2513		1357.07	48.0356
			Rooted		2.30547		48.9336	21.225
			Rooted		27.7086	Subtracted	48.9336	21.225
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Measured	Low confidence	7307		28492	21185
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	Ranked	High confidence	11621		15915	4294
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	1	Squared	Low confidence	141563		475119	333556
	cab2. [refseq;acc:nm_033419]	0	Measured	High confidence	17400000	Divided	174	0.00001
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	Measured	Low confidence	4.4149	Divided	543.5	2399.5
			Ranked		107	Subtracted	330	223
			Squared		19.4914	Divided	69.9153	1362.75
			Rooted		2.10117	Divided	23.3131	48.9847
			Rooted		25.6716	Subtracted	23.3131	48.9847
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Measured	High confidence	8126		33356.5	41482.5
	hbs1-like. [refseq;acc:nm_006620]		Ranked		107		322	215
	histone h4. [swissprot;acc:p02304]	0	Squared		71500		345123	273623
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Measured	Low confidence	8900000	Divided	89	0.00001
			Rooted		943398		9.43398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Squared		187479		1.87479
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		Measured	High confidence	6325	Subtracted	6410	85
			Rooted	High confidence	50.8706	Subtracted	60.0707	9.20014
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	Ranked	Low confidence	1.47982	Divided	330	223

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/