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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

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

network_comparison	Rank	green	description	Network Comparison Type	red
0	494	0	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	Subtracted	0
	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	492	249.857	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	494	0.00001	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	Divided	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	2411.78	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	492	5046.33	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]		5038.33
1.00223	491	22910.9	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]		22962
1.00224	489	22895.1	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]		22946.3
	490	22888.8	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]		22940.1
1.00225	487	249.857	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	486	22826.8	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]		22878.7
1.00229	485	22797.8	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]		22850.1
1.00278	484	961.098	scribble. [refseq;acc:nm_015356]		958.429
1.0029	483	20672.6	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	482	796.85	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]		793.778
1.00475	481	563.113	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	480	6396.8	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]		6428
1.00587	479	1310.67	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]		1318.37
1.00669	478	701.071	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]		705.758
1.00704	477	429	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		426
1.00716	476	1372.31	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	475	2335.98	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]		2319.24
1.00763	474	2263.85	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]		2281.12
1.00765	472	3919.25	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	471	3825.73	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]		3855.78
1.00817	470	39485	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]		39165
1.00822	469	221.565	transcription factor btf3 homolog 3. [swissprot;acc:q13892]		219.759
1.00836	468	604.911	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]		599.896
1.00856	467	2782.56	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]		2806.38
1.01082	466	1483.62	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]		1467.74
1.01102	465	6254.09	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]		6323
1.01136	464	2264.37	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.