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 7436 to 7485 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
1859	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Measured	6076.66	6463.13	1.0636
1860	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	Squared	26167.2	28674.1	1.0958
	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]	Ranked	217.895	215.547	1.01089
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Measured	6076.66	6463.13	1.0636
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Rooted	62.7784	64.64	1.02965
1861	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
	beta-catenin (pro2286). [swissprot;acc:p35222]	Squared	26746.2	29303.5	1.09561
	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Ranked	210.856	213.147	1.01087
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Measured	6076.66	6463.14	1.0636
1862	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	Ranked	210.856	213.147	1.01087
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Squared	14336.6	15706.2	1.09553
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Rooted	63.2302	65.1018	1.0296
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Measured	6076.66	6463.13	1.0636
1863	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	Squared	26779	29336.9	1.09552
	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Measured	6076.66	6463.14	1.0636
	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	Ranked	210.856	213.147	1.01087
	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	Rooted	63.2302	65.1018	1.0296
1864	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	Ranked	203.071	200.89	1.01086
	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]	Squared	26778.4	29336.2	1.09552
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Measured	6076.66	6463.14	1.0636
	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	Rooted	63.2302	65.1018	1.0296
1865	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	Ranked	221.639	224.046	1.01086
	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	Squared	26777.3	29334.8	1.09551
	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]	Rooted	63.2302	65.1018	1.0296
	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	Measured	6076.66	6463.12	1.0636
1866	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]	Squared	26776.3	29333.6	1.09551
	keratin associated protein 4.4. [refseq;acc:nm_032524]	Measured	6076.66	6463.14	1.0636
	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]	Rooted	63.2302	65.1018	1.0296
	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]	Ranked	221.725	224.133	1.01086
1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Measured	6076.66	6463.12	1.0636
	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]	Squared	26776.2	29333.5	1.09551
	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]	Ranked	203.071	200.89	1.01086
	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]	Rooted	63.2302	65.1018	1.0296
1868	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Squared	31054.8	34018.5	1.09543
	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]	Rooted	63.2302	65.1018	1.0296
	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	Measured	6076.66	6463.12	1.0636
	protein kinase nyd-sp25. [refseq;acc:nm_033516]	Ranked	207.642	209.895	1.01085
1869	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Rooted	63.7209	65.6073	1.0296
	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]	Measured	6076.66	6463.12	1.0636
	lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697]	Ranked	220.107	217.75	1.01082
	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	Squared	29358.9	32153.5	1.09519
1870	26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	Rooted	62.901	64.7621	1.02959
	lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]	Ranked	220.107	217.75	1.01082
	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566]	Squared	24718.5	27071.2	1.09518
	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Measured	6076.66	6463.13	1.0636
1871	abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	Rooted	62.1789	64.0173	1.02957
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Ranked	222.819	225.228	1.01081
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	24718.5	27071.2	1.09518
	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Measured	6076.66	6463.12	1.0636
1872	dna polymerase delta p38 subunit. [refseq;acc:nm_015584]	Ranked	222.819	225.228	1.01081

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.