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 Network Comparison Type Filtered Value Type red network_comparison Interaction Map

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	description	green	Network Comparison Type	Filtered	Value Type	red	network_comparison	Interaction Map
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Divided	0	Ranked	4294	3.70633	High confidence
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	Subtracted		Rooted	9.20014	50.8706	High confidence
		60.0707			Rooted	9.20014	50.8706	Low confidence
		6410			Measured	85	6325	High confidence
		6410			Measured	85	6325	Low confidence
	cab2. [refseq;acc:nm_033419]	7.16592	Divided		Squared	0.00001	716592	High confidence
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	32	Divided	1	Ranked	16	2	Low confidence
		32028.5	Subtracted		Measured	40899	8870.5
		242799			Squared	395912	153113
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322			Ranked	215	107	High confidence
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Divided	0	Squared	0.00001	187479	Low confidence
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	23.3131	Divided	1	Rooted	48.9847	2.10117
		23.3131	Subtracted		Rooted	48.9847	25.6716
		69.9153	Divided		Squared	1362.75	19.4914
		330	Subtracted		Ranked	223	107
		543.5	Divided		Measured	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			41482.5	8126	High confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Divided	0		364	36400000	High confidence
						364	36400000	Low confidence
					Rooted	19.0788	1907880	High confidence
					Rooted	19.0788	1907880	Low confidence
		21883	Subtracted		Ranked	8906	12977	High confidence
		21883	Subtracted			8906	12977	Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Divided			5865	2.55362	Low confidence
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	Subtracted		Squared	232467	72283	High confidence
		160184	Subtracted		Squared	232467	72283	Low confidence
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	Divided	1	Ranked	10	2.4	High confidence
		322755	Subtracted		Squared	468498	145743
	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	Divided		Rooted	21.225	2.30547
		48.9336	Subtracted		Rooted	21.225	27.7086
		1357.07	Divided		Squared	48.0356	28.2513
		2394.5	Divided		Measured	450.5	5.31521
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	28492	Subtracted		Measured	21185	7307	Low confidence
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915		0	Ranked	4294	11621	High confidence
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	475119		1	Squared	333556	141563	Low confidence
	cab2. [refseq;acc:nm_033419]	174	Divided	0	Measured	0.00001	17400000	High confidence
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	23.3131	Divided	1	Rooted	48.9847	2.10117	Low confidence
		23.3131	Subtracted		Rooted	48.9847	25.6716
		69.9153	Divided		Squared	1362.75	19.4914
		330	Subtracted		Ranked	223	107
		543.5	Divided		Measured	2399.5	4.4149
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	Subtracted		Measured	41482.5	8126	High confidence
	hbs1-like. [refseq;acc:nm_006620]	322			Ranked	215	107
	histone h4. [swissprot;acc:p02304]	345123		0	Squared	273623	71500
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398	Divided		Rooted	0.00001	943398	Low confidence
		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		Rooted	9.20014	50.8706	High confidence
		6410	Subtracted		Measured	85	6325	High confidence
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	330	Divided	1	Ranked	223	1.47982	Low confidence

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/