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

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Showing element 551 to 600 of 3228 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided

green	Rank	description	red	network_comparison
2765.82	61	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	4489.19	1.6231
	62	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
	63	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
	64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
2907.43	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	1.5137
2945.26	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]	4556.78	1.54716
2945.28	72	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	4556.79	1.54715
2945.38	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	1.54711
2945.8	74	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]	4556.99	1.54694
2978.53	130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	2234.68	1.33287
2978.57	131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	2234.73	1.33285
2980.35	132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	2236.61	1.33253
3058.57	76	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]	4599.26	1.50373
3093.6	77	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]	4612.39	1.49095
3093.78	271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	2554.89	1.21092
3144.39	391	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	3658.76	1.16358
3221.38	66	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	1991.03	1.61795
3225.65	98	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	2353.63	1.3705
	99	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
	100	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
	101	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
	102	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
	103	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
3343.62	95	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]	2397.19	1.39481
3357.6	1756	40s ribosomal protein s29. [swissprot;acc:p30054]	3582.57	1.067
3359.43	2099	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	3544.03	1.05495
	2100	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]
3360.33	1588	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	3600.99	1.07162
	1589	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
3360.39	1988	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	3559.49	1.05925
3364.84	2023	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	3560.24	1.05807
3375.34	1840	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	3591.95	1.06417
	1841	fad synthetase. [refseq;acc:nm_025207]
	1842	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
	1843	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
	1844	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]
	1845	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
	1846	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
3375.93	1834	60s ribosomal protein l11. [swissprot;acc:p39026]	3593.24	1.06437
3381.34	2152	40s ribosomal protein s23. [swissprot;acc:p39028]	3560.63	1.05302
	2153	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
3384.59	1894	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	3598.08	1.06308
3392.22	2163	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	3569.06	1.05213
3394.29	1798	60s ribosomal protein l32. [swissprot;acc:p02433]	3618.02	1.06591
3402.09	1873	40s ribosomal protein s11. [swissprot;acc:p04643]	3618.46	1.0636
3409.48	2051	60s ribosomal protein l26. [swissprot;acc:q02877]	3601.97	1.05646
3410.23	2065	60s ribosomal protein l35. [swissprot;acc:p42766]	3602.25	1.05631
3411.17	2068	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	3602.75	1.05616
3411.18	2067	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]
3411.47	2641	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	3377.01	1.0102

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.