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 144 to 193 of 8289 in total

Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
72	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	High confidence	4556.79	2945.28	1.54715
73	eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588]	Low confidence	6991.78	7848.45	1.12253
	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]	High confidence	4556.83	2945.38	1.54711
74	b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251]	Low confidence	6991.78	7848.45	1.12253
	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]	High confidence	4556.99	2945.8	1.54694
75	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]		1920.75	2907.43	1.5137
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Low confidence	11616	12942.3	1.11418
76	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		5334.13	5933.4	1.11235
	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]	High confidence	4599.26	3058.57	1.50373
77	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Low confidence	5334.13	5933.4	1.11235
	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]	High confidence	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
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Low confidence	5334.13	5933.4	1.11235
79	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	High confidence	3074.57	4567.51	1.48558
80	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]		4133.47	5945.32	1.43834
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Low confidence	5334.13	5933.4	1.11235
81	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	High confidence	4136.36	5943.56	1.43691
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	Low confidence	5528.68	6146.97	1.11183
82	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		7098.44	7884.98	1.1108
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	High confidence	4172.91	5954.48	1.42694
83	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]		4932.27	7033.29	1.42597
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Low confidence	7030.67	7794.8	1.10869
84	jun dimerization protein. [refseq;acc:nm_130469]	High confidence	4932.27	7033.29	1.42597
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Low confidence	11141.5	12351.1	1.10857
85	fos-related antigen 2. [swissprot;acc:p15408]	High confidence	4941.95	7037.11	1.42395
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Low confidence	7034.43	7797.14	1.10843
86	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	High confidence	4942.49	7037.32	1.42384
	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	Low confidence	7263.76	8046.29	1.10773
87	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	High confidence	4944.3	7038.04	1.42347
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Low confidence	7054.1	7809.38	1.10707
88	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	High confidence	2411.93	1695.45	1.42259
	serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794]	Low confidence	9631.47	10633	1.10399
89	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	High confidence	2414.22	1698.12	1.4217
	intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920]	Low confidence	9623.55	10621.3	1.10368
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]	High confidence	2414.77	1698.75	1.4215
	vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552]	Low confidence	12768	11571.4	1.10341
91	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	High confidence	2416.53	1700.8	1.42082
92	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		4117.67	5801.04	1.40882
	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	Low confidence	7297.57	8050.82	1.10322
93	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	High confidence	4245.52	5942.75	1.39977
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Low confidence	4616.06	5091.51	1.103
94	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		5674.92	6255.18	1.10225
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	High confidence	4247.86	5941.88	1.39879
95	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Low confidence	4626.46	5098.83	1.1021
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	High confidence	2397.19	3343.62	1.39481
96	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Low confidence	4630.13	5102.14	1.10194
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	High confidence	4110.14	5694.99	1.3856
97	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]		2820.51	3897.1	1.3817

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.