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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

Navigation/Query Panel:
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 Value Type Network Comparison Type Filtered Interaction Map network_comparison red

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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