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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Value Type	green	red	network_comparison
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	UBAC1	Ranked	24	10	2.4
	rad50-interacting protein 1. [refseq;acc:nm_021930]	RINT1	Measured	2394.5	450.5	5.31521
			Squared	1357.07	48.0356	28.2513
			Rooted	48.9336	21.225	2.30547
2	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]	no value	Ranked	28	15	1.86667
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	RHOBTB2	Measured	2394.5	450.5	5.31521
			Squared	1357.07	48.0356	28.2513
			Rooted	48.9336	21.225	2.30547
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	PSCD1	Ranked	28	15	1.86667
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	HLX	Measured	698.5	2597.5	3.71868
			Squared	115.48	1596.92	13.8285
			Rooted	26.4292	50.9657	1.92839
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	PSCD2	Ranked	28	15	1.86667
	hbs1-like. [refseq;acc:nm_006620]	HBS1L	Measured	698.5	2597.5	3.71868
			Squared	115.48	1596.92	13.8285
			Rooted	26.4292	50.9657	1.92839
5	cytohesin 4. [swissprot;acc:q9uia0]	PSCD4	Ranked	28	15	1.86667
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	JPH3	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	PSCD3	Ranked	28	15	1.86667
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	JPH2	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	HLX	Ranked	322	215	1.49767
	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]	SMPD2	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
8	db83 protein. [swissprot;acc:p57088]	TMEM33	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
	hbs1-like. [refseq;acc:nm_006620]	HBS1L	Ranked	322	215	1.49767
9	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	TOB2	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	XAB1	Ranked	309	212	1.45755
10	protein x 0004. [refseq;acc:nm_016301]	ATPBD1C
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	TOB1	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	DAB2IP	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	rad50-interacting protein 1. [refseq;acc:nm_021930]	RINT1	Ranked	232	337	1.45259
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	CPEB4	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	RHOBTB2	Ranked	232	337	1.45259
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	CPEB3	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414

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
- Hugo is the HGNC identifier if it exists
- 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.