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 Value Type Gene Network Comparison Type Filtered Interaction Map red network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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