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	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Value Type	Interaction Map	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]	Squared	Low confidence	0	0.00001	0.823905	82390.5
	hbs1-like. [refseq;acc:nm_006620]	Measured	High confidence	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]	Measured	Low confidence	0	0.00001	89	8900000
		Rooted				9.43398	943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	High confidence			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]	Ranked	High confidence	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]	Squared	High confidence		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]	Squared	Low confidence		0.324024	0.00001	32402.4
	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	High confidence	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]	Rooted	Low confidence	0	0.00001	7.68115	768115
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	High confidence			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]	Ranked	Low confidence		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]	Ranked	High confidence	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]	Ranked	High confidence	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]	Measured	Low confidence		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]	Measured	Low confidence		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]	Rooted	Low confidence		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.