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

Results: HTML CSV LaTeX

Showing element 932 to 981 of 3228 in total

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

Rank	green	description	red	network_comparison
932	218.013	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	225.939	1.03636
933	164.951	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	159.165	1.03635
934	233.544	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	242.024	1.03631
935	224.372	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	232.473	1.03611
936		casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
937	212.618	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	220.246	1.03588
938		splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
939	224.27	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	216.501
940	205.088	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	212.442	1.03586
941	205.083	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	212.437
942	205.088	grancalcin. [swissprot;acc:p28676]	212.442
943	205.087	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]
944	205.083	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	212.437
945	205.085	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	212.44
946	219.902	histone h4. [swissprot;acc:p02304]	227.765	1.03576
947	205.191	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	212.51	1.03567
948	209.824	target of myb protein 1. [swissprot;acc:o60784]	217.254	1.03541
949	209.826	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	217.253	1.0354
950	261.821	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	252.873	1.03539
951	209.827	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	217.253
952	209.83	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	217.252	1.03537
953	205.466	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	198.494	1.03512
954	276.773	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	267.447	1.03487
955	239.205	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	231.163	1.03479
956	204.732	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	211.812	1.03458
957	134.399	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	129.913	1.03453
958	134.406	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	129.921	1.03452
959	229.677	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	237.558	1.03431
960		zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
961	134.527	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]	130.066	1.0343
962		cyclin g2. [swissprot;acc:q16589]
963		cyclin g1 (cyclin g). [swissprot;acc:p51959]
964		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]
965	204.964	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	211.987	1.03426
966		tubby protein homolog. [swissprot;acc:p50607]
967		protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]
968		numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
969		tbc1 domain family member 5. [swissprot;acc:q92609]
970		tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971		vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972		numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973		tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974		vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975		protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	235.322	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	1.03407
977	221.421	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	228.953	1.03402
978		prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	195.386	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	202.027	1.03399
980	134.713	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	130.289	1.03396
981	200.398	exocyst complex component sec6. [swissprot;acc:o60645]	207.186	1.03387

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.