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 814 to 863 of 3228 in total

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

Rank	description	red	green	network_comparison
814	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	5641.12	6255.99	1.109
815	midasin (midas-containing protein). [swissprot;acc:q9nu22]	4483.08	4971.62	1.10897
816	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	5641.53	6256.17	1.10895
817	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	6811.2	7547.35	1.10808
818	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	6807.78	7543.28	1.10804
819	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	6805.45	7540.5	1.10801
820	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	6805.86	7540.99
821	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	6257.99	6932.95	1.10786
822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	6311.6	6989.33	1.10738
823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	6311.83	6989.6
824	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	5657.53	6263.02	1.10702
825	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
826	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	5195.58	5750.34	1.10678
827	transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403]	5172.07	5723.22	1.10656
828	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786]	5745.61	6354.75	1.10602
829	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960]
830	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]
831	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	4062.03	4492.48	1.10597
832	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]	4489.72	4965.35	1.10594
833	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
834	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	5623.18	6218.77	1.10592
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	4049	4477.43	1.10581
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	4063.64	4492.98	1.10565
838	pbk1 protein. [sptrembl;acc:o76021]	4064.23	4493.36	1.10559
839	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	7093.86	7842.67	1.10556
840	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	5786.67	6395.78	1.10526
841	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
842	loh1cr12. [refseq;acc:nm_058169]	5195.48	5741.63	1.10512
843	unr protein. [swissprot;acc:o75534]
844	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	6276.97	6934.8	1.1048
845	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
846	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747]	5607.43	6194.98	1.10478
847	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]	6776.85	7485.55	1.10458
848	wd-repeat protein bing4. [swissprot;acc:o15213]	4066.56	4491.65	1.10453
849	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	6194.15	6839.37	1.10417
850	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]
851	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	4307.12	4755.03	1.10399
852	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
853	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	4078.45	4502.32	1.10393
854	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	6562.98	7242.37	1.10352
855	ero1-like. [refseq;acc:nm_014584]
856	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	5210.58	5749.33	1.1034
857	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]
858	n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]
859	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848]
860	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]
861	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	5734.15	6326.41	1.10329
862	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	4076.72	4497.74	1.10327
863	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	5595.65	6173.23	1.10322

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.