MK5 Microarray Data

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.

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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 38536 in total

Network Comparison Type  : Divided

Rank	Interaction Map	description	Value Type	green	network_comparison	red	Filtered
7	High confidence	sedlin. [swissprot;acc:o14582]	Measured	43	4300000	0.00001	0
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]		339.5	3.39764	1153.5	1
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
	Low confidence	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		0.00001	608276	6.08276	0
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Ranked	6812	1.69451	11543
		jumonji protein. [swissprot;acc:q92833]	Squared	0.140962	14096.2	0.00001
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Ranked	240	1.325	318	1
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Measured	2113.5	2.86965	736.5
			Squared	1057.25	8.23493	128.386
			Rooted	45.9728	1.69401	27.1385
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Measured	0.00001	231962	2.31962	0
8	High confidence	db83 protein. [swissprot;acc:p57088]		339.5	3.39764	1153.5	1
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
		ero1-like. [refseq;acc:nm_014584]	Squared	0.00001	159148	1.59148	0
			Rooted		905539	9.05539
		hbs1-like. [refseq;acc:nm_006620]	Ranked	322	1.49767	215	1
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		21888	1.89918	11525	0
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Measured	43	4300000	0.00001
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		6410	75.4118	85
			Squared	19295.9	11098	1.73869
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Ranked	13216	1.68629	22286
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Rooted	0.00001	360555	3.60555
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Ranked	240	1.325	318	1
		phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Measured	5058.5	1.54317	3278
			Squared	6056.43	2.38136	2543.26
		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Rooted	47.6922	1.49674	31.8641
9	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Measured	6410	75.4118	85	0
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Squared	0.00001	85207.1	0.852071
			Rooted		774597	7.74597
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	1281.5	3.21581	398.5	1
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked	21888	1.89918	11525	0
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		309	1.45755	212	1
	Low confidence	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		44	1.31818	58
		gbp protein isoform a. [refseq;acc:nm_017870]	Rooted	47.7107	1.49599	31.8923
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Ranked	13216	1.68629	22286	0
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Squared	0.00001	4000	0.04
		jumonji protein. [swissprot;acc:q92833]	Rooted	3.00407	300407	0.00001
		n33 protein. [swissprot;acc:q13454]	Measured	5058.5	1.54317	3278	1
			Squared	6056.43	2.38136	2543.26
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Measured	10.6048	36.1876	383.762	0
10	High confidence	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Ranked	14178.1	1.88805	7509.39
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Squared	0.823905	82390.5	0.00001
			Rooted	7.68115	768115
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured	6410	75.4118	85
		protein x 0004. [refseq;acc:nm_016301]	Ranked	309	1.45755	212	1
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	1281.5	3.21581	398.5

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.