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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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