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

Results: HTML CSV LaTeX

Showing element 133 to 182 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
67	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	6475.5	10307.5	1.59177
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Subtracted	17756.5	14007.3	3749.2
68	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	6475.5	10307.5	1.59177
	cyclin g2. [swissprot;acc:q16589]	Subtracted	17738.6	13995.7	3742.9
69	cyclin g1 (cyclin g). [swissprot;acc:p51959]		17738.5	13995.6
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided	6475.5	10307.5	1.59177
70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	Subtracted	17738.5	13995.7	3742.8
71	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Divided	4556.78	2945.26	1.54716
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Subtracted	17738.5	13995.7	3742.8
72	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]		17710.9	13977.7	3733.2
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Divided	4556.79	2945.28	1.54715
73	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]		4556.83	2945.38	1.54711
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Subtracted	22268.8	18560.4	3708.4
74	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		20446.1	24136.4	3690.3
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Divided	4556.99	2945.8	1.54694
75	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Subtracted	20446.1	24136.4	3690.3
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	Divided	1920.75	2907.43	1.5137
76	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Subtracted	20446.1	24136.4	3690.3
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Divided	4599.26	3058.57	1.50373
77	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	20446.1	24136.4	3690.3
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Divided	4612.39	3093.6	1.49095
78	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		4800.81	7132.71	1.48573
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Subtracted	20446.1	24136.4	3690.3
79	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	3074.57	4567.51	1.48558
80	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Subtracted	20446.1	24136.4	3690.3
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Divided	4133.47	5945.32	1.43834
81	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	20446.1	24136.4	3690.3
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Divided	4136.36	5943.56	1.43691
82	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Subtracted	20446.1	24136.4	3690.3
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Divided	4172.91	5954.48	1.42694
83	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Subtracted	21644.2	18098.7	3545.5
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Divided	4932.27	7033.29	1.42597
84	jun dimerization protein. [refseq;acc:nm_130469]
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Subtracted	21632.5	18090	3542.5
85	fos-related antigen 2. [swissprot;acc:p15408]	Divided	4941.95	7037.11	1.42395
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Subtracted	21370.8	17896.5	3474.3
86	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Divided	4942.49	7037.32	1.42384
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Subtracted	21370.8	17896.5	3474.3
87	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Divided	4944.3	7038.04	1.42347
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Subtracted	20287.2	17083.8	3203.4
88	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Divided	2411.93	1695.45	1.42259
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Subtracted	16074	12888.4	3185.6
89	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Divided	2414.22	1698.12	1.4217
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Subtracted	16071.6	12886.8	3184.8
90	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Divided	2414.77	1698.75	1.4215
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Subtracted	16071.6	12886.8	3184.8
91	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Divided	2416.53	1700.8	1.42082
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Subtracted	16070.4	12886	3184.4

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.