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	Interaction Map	Value Type	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Interaction Map	Value Type	Filtered	red	green	network_comparison
4	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]	Low confidence	Squared	0	0.00001	0.823905	82390.5
	hbs1-like. [refseq;acc:nm_006620]	High confidence	Measured	1	2597.5	698.5	3.71868
			Squared		1596.92	115.48	13.8285
			Rooted		50.9657	26.4292	1.92839
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	Measured	0	0.00001	89	8900000
			Rooted			9.43398	943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence	Measured			89	8900000
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence		1	2399.5	543.5	4.4149
			Squared		1362.75	69.9153	19.4914
			Rooted		48.9847	23.3131	2.10117
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Ranked	0	8906	21883	2.45711
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Low confidence			9607	20617	2.14604
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	Squared		0.00001	2.81207	281207
			Rooted			10.4403	1044030
5	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence	Squared		0.324024	0.00001	32402.4
	cytohesin 4. [swissprot;acc:q9uia0]	High confidence	Ranked	1	15	28	1.86667
	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]	Low confidence	Rooted	0	0.00001	7.68115	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence	Squared			1.87479	187479
			Rooted			9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Measured			89	8900000
	jumonji protein. [swissprot;acc:q92833]	Low confidence				17.5166	1751660
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence		1	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	Ranked		223	330	1.47982
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Measured		736.5	2113.5	2.86965
			Squared		128.386	1057.25	8.23493
			Rooted		27.1385	45.9728	1.69401
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	High confidence	Ranked	0	5510.5	11965.7	2.17144
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence			10889.4	19873	1.82499
6	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		Rooted		6.08276	0.00001	608276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Squared		0.324024		32402.4
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence	Ranked	1	15	28	1.86667
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		Measured	0	0.00001	89	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Squared			1.87479	187479
			Rooted			9.43398	943398
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	Measured		13	0.00001	1300000
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence		1	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence	Measured		736.5	2113.5	2.86965
			Squared		128.386	1057.25	8.23493
			Rooted		27.1385	45.9728	1.69401
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Ranked		318	240	1.325
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]			0	5575.71	9583.37	1.71877
	ubiquitin protein ligase. [refseq;acc:nm_130466]	High confidence			7523	15339.2	2.03897
7	cab2. [refseq;acc:nm_033419]				21866	10950	1.99689
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence	Rooted		6.08276	0.00001	608276
	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		11543	6812	1.69451
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence		1	215	322	1.49767

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.