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

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Showing element 80 to 129 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
40	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	0	3845	5699	1.48218
41	60s ribosomal protein l21. [swissprot;acc:p46778]		9994.33	6758.83	1.47871
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	322	253	1.27273
42	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	8158	5530.5	1.47509
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	1	204.641	160.957	1.2714
43	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	0	12143.8	8356.02	1.4533
	jun dimerization protein. [refseq;acc:nm_130469]	1	204.641	160.957	1.2714
44	fos-related antigen 2. [swissprot;acc:p15408]			161.046	1.2707
	serpin b12. [swissprot;acc:q96p63]	0	14604.2	21138.6	1.44743
45	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]		14592	21113.7	1.44694
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	1	204.641	161.051	1.27066
46	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	12941.7	18499.2	1.42943
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	1	204.642	161.068	1.27053
47	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	0	12941.7	18499.2	1.42943
	gbp protein isoform a. [refseq;acc:nm_017870]	1	325.586	256.492	1.26938
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		65.4586	83.0461	1.26868
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	0	9830	6909	1.42278
49	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	1	133	105	1.26667
	brain protein 16. [refseq;acc:nm_016458]	0	6890.54	4854.99	1.41927
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	1	133	105	1.26667
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	0	9249.73	13091.4	1.41533
51	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]		7168	5102	1.40494
	spermatogenesis associated 6. [refseq;acc:nm_019073]	1	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	0	3284	4554.5	1.38688
53	transcription factor jun-b. [swissprot;acc:p17275]	1	201.144	158.868	1.26611
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	0	3284	4554.5	1.38688
54	syntaxin 10 (syn10). [swissprot;acc:o60499]		13884.4	19014.6	1.36949
	transcription factor jun-d. [swissprot;acc:p17535]	1	200.941	158.941	1.26425
55	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		320.927	254.434	1.26134
	sedlin. [swissprot;acc:o14582]	0	22440	16388	1.36929
56	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	266.856	336.233	1.25998
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	22440	16388	1.36929
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1	266.856	336.233	1.25998
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	0	8152.55	11134.8	1.36581
58	dead-box protein. [refseq;acc:nm_018665]		10628.3	14486	1.36296
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1	266.863	336.191	1.25979
59	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	0	15863.6	11662.3	1.36025
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	1	266.863	336.19	1.25978
60	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0	11761	15924	1.35397
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	266.864	336.184	1.25976
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]			336.182	1.25975
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	0	15352	11346.5	1.35302
62	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]		9418.7	12695.6	1.34791
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1	266.865	336.181	1.25974
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]			336.178	1.25973
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	0	8519.83	11453	1.34428
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	266.868	336.159	1.25965
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	15264	20387	1.33563
65	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]		7853.67	10406.3	1.32502

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.