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

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Showing element 818 to 867 of 3228 in total

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

Rank	network_comparison	description	red	green
818	1.10804	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	6807.78	7543.28
819	1.10801	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	6805.45	7540.5
820		ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	6805.86	7540.99
821	1.10786	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	6257.99	6932.95
822	1.10738	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	6311.6	6989.33
823		retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	6311.83	6989.6
824	1.10702	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	5657.53	6263.02
825		atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
826	1.10678	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
827	1.10656	transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403]	5172.07	5723.22
828	1.10602	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786]	5745.61	6354.75
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	1.10597	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	4062.03	4492.48
832	1.10594	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
833		zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
834	1.10592	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	5623.18	6218.77
835		28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]
836	1.10581	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	4049	4477.43
837	1.10565	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	4063.64	4492.98
838	1.10559	pbk1 protein. [sptrembl;acc:o76021]	4064.23	4493.36
839	1.10556	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	7093.86	7842.67
840	1.10526	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	5786.67	6395.78
841		mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
842	1.10512	loh1cr12. [refseq;acc:nm_058169]	5195.48	5741.63
843		unr protein. [swissprot;acc:o75534]
844	1.1048	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	6276.97	6934.8
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	1.10478	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
847	1.10458	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]	6776.85	7485.55
848	1.10453	wd-repeat protein bing4. [swissprot;acc:o15213]	4066.56	4491.65
849	1.10417	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
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	1.10399	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	4307.12	4755.03
852		casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
853	1.10393	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	4078.45	4502.32
854	1.10352	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	6562.98	7242.37
855		ero1-like. [refseq;acc:nm_014584]
856	1.1034	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
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	1.10329	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
862	1.10327	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	4076.72	4497.74
863	1.10322	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	5595.65	6173.23
864		ring finger protein 44. [refseq;acc:nm_014901]
865		phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]
866		ring finger protein 38. [refseq;acc:nm_022781]
867		phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]

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.