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	network_comparison	green

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Showing element 894 to 943 of 3228 in total

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

Rank	description	red	network_comparison	green
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	217.491	1.03902	209.323
895	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	230.811	1.03888	239.785
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	272.878	1.03882	283.472
898	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	229.171	1.03874	238.048
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
901	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	237.62	1.03872	228.762
902	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
903	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	246.354	1.03849	237.223
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
905	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	230.768	1.03841	239.632
906	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	230.764	1.03838	239.62
907	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	223.906	1.03827	215.653
908	tax interaction protein 1. [refseq;acc:nm_014604]
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	142.077	1.03823	136.846
910	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	217.168	1.03805	209.207
911	ero1-like. [refseq;acc:nm_014584]
912	wd-repeat protein 3. [swissprot;acc:q9unx4]	243.896	1.03803	234.96
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	210.863	1.03801	218.878
914	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]
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	146.036	1.03798	140.692
916	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]	232.512	1.03774	241.288
917	parafibromin. [refseq;acc:nm_024529]	239.704	1.03772	230.991
918	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	212.952	1.03731	205.292
919	midasin (midas-containing protein). [swissprot;acc:q9nu22]	237.218	1.03725	228.698
920	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	236.741	1.0372	245.547
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	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	215.665	1.03714	207.942
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	217.942	1.03713	210.139
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	225.976	1.03651	218.017
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	225.955	1.03642	218.015
930	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	1.0364	239.778
931	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	159.13	1.03637	164.917
932	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	225.939	1.03636	218.013
933	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	159.165	1.03635	164.951
934	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	242.024	1.03631	233.544
935	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	1.03611	224.372
936	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
937	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	220.246	1.03588	212.618
938	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
939	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	216.501		224.27
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	212.442	1.03586	205.088
941	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	grancalcin. [swissprot;acc:p28676]	212.442		205.088
943	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]			205.087

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.