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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 927 to 976 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
927	no value	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	217.942	210.139	1.03713
928	MTRF1	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	225.976	218.017	1.03651
929	MPDU1	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	225.955	218.015	1.03642
930	PKM2	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	231.357	239.778	1.0364
931	BHLHB4	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	159.13	164.917	1.03637
932	MTRF1L	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	225.939	218.013	1.03636
933	BHLHB5	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	159.165	164.951	1.03635
934	NOL6	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	242.024	233.544	1.03631
935	no value	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	224.372	1.03611
936		casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
937	SF3A3	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	220.246	212.618	1.03588
938	SF3A1	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
939	BRCA1	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	216.501	224.27
940	CAPNS1	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	212.442	205.088	1.03586
941	ARID1A	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	205.083
942	GCA	grancalcin. [swissprot;acc:p28676]	212.442	205.088
943	SRI	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]		205.087
944	PDCD6	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	212.437	205.083
945	ARID1B	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	212.44	205.085
946	no value	histone h4. [swissprot;acc:p02304]	227.765	219.902	1.03576
947	SORBS2	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	212.51	205.191	1.03567
948	TOM1	target of myb protein 1. [swissprot;acc:o60784]	217.254	209.824	1.03541
949	no value	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	217.253	209.826	1.0354
950	ERCC5	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	252.873	261.821	1.03539
951	TRIO	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	217.253	209.827
952	TOM1L2	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	217.252	209.83	1.03537
953	EXOSC10	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	205.466	1.03512
954	GSTZ1	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	276.773	1.03487
955	MRPL27	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	231.163	239.205	1.03479
956	SORBS3	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	211.812	204.732	1.03458
957	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	129.913	134.399	1.03453
958	RAF1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	129.921	134.406	1.03452
959	no value	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	229.677	1.03431
960	ZRF1	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
961	PPP2R5E	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	134.527	1.0343
962	CCNG2	cyclin g2. [swissprot;acc:q16589]
963	CCNG1	cyclin g1 (cyclin g). [swissprot;acc:p51959]
964	PPP2R5A	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	PARD6G	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	211.987	204.964	1.03426
966	TUB	tubby protein homolog. [swissprot;acc:p50607]
967	PRKCI	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	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
969	TBC1D5	tbc1 domain family member 5. [swissprot;acc:q92609]
970	TULP1	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971	VPS29	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972	NUMBL	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973	TULP3	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974	VPS35	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975	PRKCZ	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	WDR36	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	235.322	1.03407

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
- Hugo is the HGNC identifier if it exists
- 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.