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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

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Showing element 1 to 50 of 29840 in total

Filtered  : 0
Value Type  : Measured
Interaction Map  : High confidence

network_comparison	green	Rank	description	red	Network Comparison Type
0	0	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0	Subtracted
		495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
		496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
		497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
		498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
		501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
		502	brca1 associated protein. [refseq;acc:nm_006768]
0.562	249.857	492	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	250.419
		493	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1	0.00001	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0.00001	Divided
		495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
		496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
		497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
		498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
		501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
		502	brca1 associated protein. [refseq;acc:nm_006768]
1.00059	2411.78	493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	2410.35
1.00159	5046.33	492	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	5038.33
1.00223	22910.9	491	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	22962
1.00224	22888.8	490	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	22940.1
	22895.1	489	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	22946.3
1.00225	249.857	487	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	250.419
		488	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1.00227	22826.8	486	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	22878.7
1.00229	22797.8	485	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	22850.1
1.00278	961.098	484	scribble. [refseq;acc:nm_015356]	958.429
1.0029	20672.6	483	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	20612.9
1.00387	796.85	482	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	793.778
1.00475	563.113	481	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	565.785
1.00488	6396.8	480	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	6428
1.00587	1310.67	479	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1318.37
1.00669	701.071	478	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	705.758
1.00704	429	477	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	426
1.00716	1372.31	476	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	1362.55
1.00722	2335.98	475	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	2319.24
1.00763	2263.85	474	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	2281.12
1.00765	3919.25	472	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	3889.5
		473	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
1.00785	3825.73	471	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	3855.78
1.00817	39485	470	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	39165
1.00822	221.565	469	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	219.759
1.00836	604.911	468	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	599.896
1.00856	2782.56	467	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	2806.38
1.01082	1483.62	466	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	1467.74
1.01102	6254.09	465	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	6323
1.01136	2264.37	464	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	2290.09

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.