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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Filtered	green	Value Type	Interaction Map	red	network_comparison
7	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	1.87479	Squared	High confidence	0.00001	187479
			9.43398	Rooted			943398
	jumonji protein. [swissprot;acc:q92833]		0.140962	Squared	Low confidence		14096.2
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1	240	Ranked		318	1.325
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]		45.9728	Rooted		27.1385	1.69401
			1057.25	Squared		128.386	8.23493
			2113.5	Measured		736.5	2.86965
	sedlin. [swissprot;acc:o14582]	0	43		High confidence	0.00001	4300000
	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]	1	18.4255	Rooted		33.9632	1.84327
			27.2805	Squared		314.926	11.544
			339.5	Measured		1153.5	3.39764
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0	0.00001		Low confidence	2.31962	231962
8	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		6410			85	75.4118
			19295.9	Squared		1.73869	11098
	db83 protein. [swissprot;acc:p57088]	1	18.4255	Rooted	High confidence	33.9632	1.84327
			27.2805	Squared		314.926	11.544
			339.5	Measured		1153.5	3.39764
	ero1-like. [refseq;acc:nm_014584]	0	0.00001	Squared		1.59148	159148
				Rooted		9.05539	905539
	hbs1-like. [refseq;acc:nm_006620]	1	322	Ranked		215	1.49767
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	13216		Low confidence	22286	1.68629
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		0.00001	Rooted		3.60555	360555
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		21888	Ranked	High confidence	11525	1.89918
	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	1	240		Low confidence	318	1.325
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]		5058.5	Measured		3278	1.54317
			6056.43	Squared		2543.26	2.38136
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	43	Measured	High confidence	0.00001	4300000
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1	47.6922	Rooted	Low confidence	31.8641	1.49674
9	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		44	Ranked		58	1.31818
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	6410	Measured	High confidence	85	75.4118
	gbp protein isoform a. [refseq;acc:nm_017870]	1	47.7107	Rooted	Low confidence	31.8923	1.49599
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	13216	Ranked		22286	1.68629
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		0.00001	Squared		0.04	4000
	jumonji protein. [swissprot;acc:q92833]		3.00407	Rooted		0.00001	300407
	n33 protein. [swissprot;acc:q13454]	1	5058.5	Measured		3278	1.54317
			6056.43	Squared		2543.26	2.38136
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	0.00001		High confidence	0.852071	85207.1
				Rooted		7.74597	774597
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	35.798			19.9625	1.79326
			388.696	Squared		37.5863	10.3414
			1281.5	Measured		398.5	3.21581
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	21888	Ranked		11525	1.89918
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]		10.6048	Measured	Low confidence	383.762	36.1876
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	309	Ranked	High confidence	212	1.45755
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	14178.1			7509.39	1.88805
	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]		0.823905	Squared		0.00001	82390.5
			7.68115	Rooted			768115
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		13216	Ranked	Low confidence	22286	1.68629
	implantation-associated protein. [refseq;acc:nm_032121]	1	5058.5	Measured		3278	1.54317
			6056.43	Squared		2543.26	2.38136

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.