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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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