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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 29840 in total

Interaction Map  : High confidence

Rank	description	Network Comparison Type	Value Type	Filtered	green	network_comparison	red
4	cytohesin 4. [swissprot;acc:q9uia0]	Subtracted	Measured	1	33356.5	8126	41482.5
	hbs1-like. [refseq;acc:nm_006620]	Divided			698.5	3.71868	2597.5
			Squared		115.48	13.8285	1596.92
			Rooted		26.4292	1.92839	50.9657
		Subtracted				24.5365
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Measured	0	89	8900000	0.00001
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Ranked		21883	2.45711	8906
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	Rooted		7.61577	21.6929	29.3087
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		Ranked		21888	10363	11525
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	Squared		2.81207	281207	0.00001
			Rooted		10.4403	1044030
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	Ranked	1	232	105	337
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]		Squared	0	105900	30453.3	75446.7
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		Measured		21730	3026	18704
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Rooted	1	168.796	23.245	145.551
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Measured		33356.5	8126	41482.5
	cytohesin 4. [swissprot;acc:q9uia0]	Divided	Ranked		28	1.86667	15
		Subtracted	Squared		263351	143938	407289
	histone h4. [swissprot;acc:p02304]		Measured	0	24446.3	2673.2	21773.1
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Squared		1.87479	187479	0.00001
			Rooted		9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Measured		89	8900000
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			1	339.5	3.39764	1153.5
			Squared		27.2805	11.544	314.926
			Rooted		18.4255	1.84327	33.9632
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted		0	0	19.0788	19.0788
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		Ranked		21888	10363	11525
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Divided			11965.7	2.17144	5510.5
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted		1	309	97	212
	zinc finger protein 277. [swissprot;acc:q9nrm2]		Squared	0	105900	30453.3	75446.7
6	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]				102814	29733.2	73080.8
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	Ranked	1	28	1.86667	15
		Subtracted	Squared		263351	143938	407289
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	Measured	0	89	8900000	0.00001
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Squared		1.87479	187479
			Rooted		9.43398	943398
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		Measured	1	339.5	3.39764	1153.5
			Squared		27.2805	11.544	314.926
			Rooted		18.4255	1.84327	33.9632
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	Ranked	0	14977	9112	5865
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		Rooted	1	168.796	23.245	145.551
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]			0	27.8029	15.6374	12.1655
	protein x 0004. [refseq;acc:nm_016301]		Ranked	1	309	97	212
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		Measured		36927.5	7563	44490.5
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]			0	15605.1	2430.4	13174.7
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Divided	Ranked		15339.2	2.03897	7523
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	Measured	1	28492	7307	21185
	cab2. [refseq;acc:nm_033419]	Divided	Ranked	0	10950	1.99689	21866
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]			1	322	1.49767	215
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		Squared	0	1.87479	187479	0.00001

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.