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 1051 to 1100 of 8289 in total

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

Rank	description	Interaction Map	red	green	network_comparison
526	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	High confidence	250.538	234.401	1.06884
	solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0]	Low confidence	205.549	199.117	1.0323
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	High confidence	248.56	232.579	1.06871
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Low confidence	208.004	201.497	1.03229
528	solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168]		205.543	199.115	1.03228
	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	High confidence	222.146	237.393	1.06864
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]		251.653	235.506	1.06856
	zinc finger protein 183-like 1. [refseq;acc:nm_178861]	Low confidence	205.116	198.702	1.03228
530	solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [swissprot;acc:p11169]		205.541	199.114
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	High confidence	227.483	212.994	1.06803
531	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]		223.356	209.149	1.06793
	solute carrier family 2, facilitated glucose transporter, member 4 (glucose transporter type 4, insulin-responsive). [swissprot;acc:p14672]	Low confidence	205.54	199.114	1.03227
532	glucose transporter 14. [refseq;acc:nm_153449]		205.541	199.115
	zinc finger-like protein 9. [refseq;acc:nm_033414]	High confidence	250.942	235.004	1.06782
533	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
	solute carrier family 2, facilitated glucose transporter, member 1 (glucose transporter type 1, erythrocyte/brain) (hepg2 glucose transporter). [swissprot;acc:p11166]	Low confidence	205.533	199.112	1.03225
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	High confidence	250.942	235.004	1.06782
	zinc finger protein 216. [swissprot;acc:o76080]	Low confidence	184.361	178.613	1.03218
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	High confidence	236.662	252.708	1.0678
	protein associated with prk1. [refseq;acc:nm_019006]	Low confidence	184.361	178.613	1.03218
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	High confidence	242.531	227.136	1.06778
	ran binding protein 9; novel centrosomal protein ranbpm; ran binding protein, centrosomal. [refseq;acc:nm_005493]	Low confidence	203.519	197.195	1.03207
537	megf11 protein. [refseq;acc:nm_032445]		207.951	201.517	1.03193
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	High confidence	229.803	215.301	1.06736
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]		237.627	253.604	1.06724
	megf10 protein. [refseq;acc:nm_032446]	Low confidence	207.949	201.517	1.03192
539	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	High confidence	236.964	252.86	1.06708
	protein x 0001. [refseq;acc:nm_016302]	Low confidence	199.661	193.489	1.0319
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	High confidence	222.156	208.201	1.06703
		Low confidence	206.406	200.027	1.03189
541	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]	High confidence	222.156	208.201	1.06703
		Low confidence	206.406	200.027	1.03189
542	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]	High confidence	222.156	208.201	1.06703
		Low confidence	206.406	200.027	1.03189
543	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]	High confidence	222.156	208.201	1.06703
		Low confidence	206.406	200.027	1.03189
544	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]	High confidence	222.156	208.201	1.06703
		Low confidence	206.406	200.027	1.03189
545	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]		202.949	196.678	1.03188
	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	High confidence	248.866	233.287	1.06678
546	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]		207.222	194.262	1.06671
	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	Low confidence	202.949	196.678	1.03188
547	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	High confidence	207.26	194.346	1.06645
	sestrin 3. [swissprot;acc:p58005]	Low confidence	203.305	197.023	1.03188
548	flotillin-1. [swissprot;acc:o75955]		203.303	197.022
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	High confidence	207.26	194.346	1.06645
549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
	sestrin 2 (hi95). [swissprot;acc:p58004]	Low confidence	203.306	197.024	1.03188
550	sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5]		203.299	197.018
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	High confidence	207.26	194.346	1.06645

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.