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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

network_comparison	Rank	description	green	red
1	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	0.00001
	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	493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	2411.78	2410.35
1.00159	492	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	5046.33	5038.33
1.00223	491	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	22910.9	22962
1.00224	489	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	22895.1	22946.3
	490	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	22888.8	22940.1
1.00225	487	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	249.857	250.419
	488	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1.00227	486	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	22826.8	22878.7
1.00229	485	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	22797.8	22850.1
1.00278	484	scribble. [refseq;acc:nm_015356]	961.098	958.429
1.0029	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]	20672.6	20612.9
1.00387	482	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	796.85	793.778
1.00475	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]	563.113	565.785
1.00488	480	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	6396.8	6428
1.00587	479	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1310.67	1318.37
1.00669	478	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	701.071	705.758
1.00704	477	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	429	426
1.00716	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]	1372.31	1362.55
1.00722	475	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	2335.98	2319.24
1.00763	474	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	2263.85	2281.12
1.00765	472	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	3919.25	3889.5
	473	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
1.00785	471	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	3825.73	3855.78
1.00817	470	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	39485	39165
1.00822	469	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	221.565	219.759
1.00836	468	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	604.911	599.896
1.00856	467	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	2782.56	2806.38
1.01082	466	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	1483.62	1467.74
1.01102	465	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	6254.09	6323
1.01136	464	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	2264.37	2290.09
1.01163	463	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	1248.14	1262.65
1.01202	462	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	11305	11170.7
1.01229	461	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	1892.44	1915.69
1.01259	460	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	3739.55	3693.07
1.01266	459	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	3821.87	3774.08
1.01327	458	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	2668.56	2633.61
1.01341	457	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	1541.69	1562.36
1.01343	456	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	17126	17356
1.01362	455	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	2371.24	2403.53
1.01402	454	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	3174.79	3219.3
1.01438	453	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	1356.52	1337.29

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.