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

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Showing element 918 to 967 of 3228 in total

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

Rank	green	red	description	network_comparison
918	205.292	212.952	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	1.03731
919	228.698	237.218	midasin (midas-containing protein). [swissprot;acc:q9nu22]	1.03725
920	245.547	236.741	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	1.0372
921			rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]
922			map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]
923			map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
924			meiotic recombination protein spo11. [swissprot;acc:q9y5k1]
925	207.942	215.665	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	1.03714
926	210.139	217.942	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	1.03713
927			microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
928	218.017	225.976	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	1.03651
929	218.015	225.955	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	1.03642
930	239.778	231.357	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	1.0364
931	164.917	159.13	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	1.03637
932	218.013	225.939	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	1.03636
933	164.951	159.165	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	1.03635
934	233.544	242.024	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	1.03631
935	224.372	232.473	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]	1.03611
936			casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
937	212.618	220.246	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	1.03588
938			splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
939	224.27	216.501	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]
940	205.088	212.442	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	1.03586
941	205.083	212.437	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]
942	205.088	212.442	grancalcin. [swissprot;acc:p28676]
943	205.087		sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]
944	205.083	212.437	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
945	205.085	212.44	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]
946	219.902	227.765	histone h4. [swissprot;acc:p02304]	1.03576
947	205.191	212.51	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	1.03567
948	209.824	217.254	target of myb protein 1. [swissprot;acc:o60784]	1.03541
949	209.826	217.253	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	1.0354
950	261.821	252.873	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	1.03539
951	209.827	217.253	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]
952	209.83	217.252	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	1.03537
953	205.466	198.494	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]	1.03512
954	276.773	267.447	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	1.03487
955	239.205	231.163	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	1.03479
956	204.732	211.812	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	1.03458
957	134.399	129.913	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	1.03453
958	134.406	129.921	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	1.03452
959	229.677	237.558	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]	1.03431
960			zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
961	134.527	130.066	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]	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	211.987	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	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]

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.