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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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