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

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Showing element 51 to 100 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

network_comparison	Rank	description	green	Value Type	red	Interaction Map
1	841	gamma-glutamyltransferase. [sptrembl;acc:q14390]	0.00001	Squared	0.00001	Low confidence
				Rooted
	842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]		Measured
				Ranked
				Squared
				Rooted
	843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]		Measured
				Ranked
				Squared
				Rooted
1.00005	836	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	1589.95	Measured	1589.87
1.00007		protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	13844.1	Ranked	13845
1.00008	492	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	62.8986	Rooted	62.8936	High confidence
	493	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
1.0001	835	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	1573.69	Measured	1573.54	Low confidence
1.00015	834	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	2710.41		2710.81
1.00017	492	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	6792.32	Squared	6791.15	High confidence
1.0002	833	ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686]	9357.07	Measured	9355.21	Low confidence
1.00023	836	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	27.1942	Rooted	27.188
1.00032	835	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	11478.8	Ranked	11482.5
1.00033	832	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	3507.42	Measured	3506.27
1.00038	835	ero1-like. [refseq;acc:nm_014584]	33.6926	Rooted	33.7054
1.00041	491	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	42.6315		42.6139	High confidence
	834	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	16322.5	Ranked	16315.8	Low confidence
1.00059	493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	2411.78	Measured	2410.35	High confidence
	834	putative forkhead box protein kiaa1041. [swissprot;acc:q9upw0]	25.9014	Rooted	25.9167	Low confidence
1.00065	831	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]	1242.41	Measured	1243.22
1.00068	833	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	28.7389	Rooted	28.7585
1.00071	835	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	26139.1	Squared	26120.5
1.00074	830	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	3462.18	Measured	3464.75
1.00078	833	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	12904.6	Ranked	12894.5
1.00082	832	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	28.7	Rooted	28.7235
1.00085	831	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	22.2092		22.228
1.00086	829	alpha-nac protein. [sptrembl;acc:q9h009]	1465.37	Measured	1464.11
1.0009	834	scratch; scratch 1. [refseq;acc:nm_031309]	3041.93	Squared	3044.68
1.00094	490	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	24.4079	Rooted	24.4309	High confidence
	831	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	11872.8	Ranked	11861.6	Low confidence
	832	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	2668.83		2671.33
1.00101	491	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	2873.96	Squared	2871.07	High confidence
	833	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	15881.6		15865.5	Low confidence
1.00108	832	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	3022.35		3025.6
1.00111	830	forkhead box protein j1 (forkhead-related protein fkhl13) (hepatocyte nuclear factor 3 forkhead homolog 4) (hfh-4). [swissprot;acc:q92949]	25.883	Rooted	25.9117
1.00123	499	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	9069.58	Ranked	9080.73	High confidence
1.00124	828	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	1464.85	Measured	1463.03	Low confidence
	829	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	28.6975	Rooted	28.733
1.00128	489	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	22.9676		22.997	High confidence
	828	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	27.3392		27.3043	Low confidence
1.0013	827	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	1673.2	Measured	1675.38
1.00133	830	scratch; scratch 1. [refseq;acc:nm_031309]	12881.3	Ranked	12864.2
1.00138	826	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	14901.7	Measured	14922.2

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.