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 1813 to 1862 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
907	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	Divided	223.906	215.653	1.03827
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Subtracted	225.976	218.017	7.959
908	sedlin. [swissprot;acc:o14582]		129.219	121.261	7.958
	tax interaction protein 1. [refseq;acc:nm_014604]	Divided	223.906	215.653	1.03827
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]		142.077	136.846	1.03823
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Subtracted	129.219	121.261	7.958
910	bet3 homolog. [swissprot;acc:o43617]
	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	Divided	217.168	209.207	1.03805
911	ero1-like. [refseq;acc:nm_014584]
	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Subtracted	225.955	218.015	7.94
912	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]		225.939	218.013	7.926
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Divided	243.896	234.96	1.03803
913	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Subtracted	243.297	235.373	7.924
	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	Divided	210.863	218.878	1.03801
914	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]	Subtracted	237.558	229.677	7.881
	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399]	Divided	210.863	218.878	1.03801
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]		146.036	140.692	1.03798
	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]	Subtracted	237.558	229.677	7.881
916	histone h4. [swissprot;acc:p02304]		227.765	219.902	7.863
	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]	Divided	232.512	241.288	1.03774
917	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	86.7483	78.8995	7.8488
	parafibromin. [refseq;acc:nm_024529]	Divided	239.704	230.991	1.03772
918	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Subtracted	217.942	210.139	7.803
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Divided	212.952	205.292	1.03731
919	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Subtracted	217.942	210.139	7.803
	midasin (midas-containing protein). [swissprot;acc:q9nu22]	Divided	237.218	228.698	1.03725
920	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	Subtracted	216.501	224.27	7.769
	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	Divided	236.741	245.547	1.0372
921	rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]
	wd-repeat protein bing4. [swissprot;acc:o15213]	Subtracted	243.227	235.475	7.752
922	map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	Divided	236.741	245.547	1.0372
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Subtracted	215.665	207.942	7.723
923	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]		193.114	185.412	7.702
	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]	Divided	236.741	245.547	1.0372
924	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Subtracted	238.725	231.059	7.666
925	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Divided	215.665	207.942	1.03714
	protein bap28. [swissprot;acc:q9h583]	Subtracted	244.312	236.647	7.665
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Divided	217.942	210.139	1.03713
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Subtracted	212.952	205.292	7.66
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Divided	217.942	210.139	1.03713
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Subtracted	220.246	212.618	7.628
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Divided	225.976	218.017	1.03651
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Subtracted	220.246	212.618	7.628
929	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]		243.045	235.422	7.623
	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Divided	225.955	218.015	1.03642
930	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Subtracted	233.402	225.782	7.62
	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	Divided	231.357	239.778	1.0364
931	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]		159.13	164.917	1.03637
	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Subtracted	228.953	221.421	7.532

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.