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

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Showing element 1501 to 1550 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
376	Measured	44050 protein. [refseq;acc:nm_178832]	17385.9	14889.2	1.16769
	Ranked	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	234.945	1.09395
	Squared	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	46021.4	56813.2	1.2345
	Rooted	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	50.2554	45.5688	1.10285
377	Measured	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	17385.9	14889.2	1.16769
	Ranked	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	265.481	1.09391
	Squared	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	33044.9	40781.4	1.23412
	Rooted	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	50.2554	45.5687	1.10285
378	Measured	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	12471.7	14561.7	1.16758
	Ranked	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	265.365	1.09387
	Squared	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	15034.5	18552.2	1.23398
	Rooted	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	50.5816	45.8738	1.10263
379	Measured	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	6704.44	7811.45	1.16512
	Ranked	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	264.163	1.0938
	Squared	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	33010.8	40732.2	1.23391
	Rooted	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	59.5128	65.604	1.10235
380	Measured	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	12998.5	15138.2	1.16461
	Ranked	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	264.79	1.09368
	Squared	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	32991.5	40704.5	1.23379
	Rooted	calcyphosine. [swissprot;acc:q13938]	59.5128	65.604	1.10235
381	Measured	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	5246.01	6109.31	1.16456
	Ranked	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	183.423	1.09357
	Squared	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	32987.4	40698.5	1.23376
	Rooted	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	59.5128	65.604	1.10235
382	Measured	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	4533.74	5279.4	1.16447
	Ranked	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	200.791	183.66	1.09328
	Squared	rna-binding protein. [refseq;acc:nm_019027]	15043.7	18560.1	1.23375
	Rooted	40s ribosomal protein s23. [swissprot;acc:p39028]	49.8325	45.2077	1.1023
383	Measured	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	4533.74	5279.4	1.16447
	Ranked	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	237.862	217.739	1.09242
	Squared	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	15043.7	18560.1	1.23375
	Rooted	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	49.8325	45.2077	1.1023
384	Measured	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	4533.74	5279.4	1.16447
	Ranked	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	266.421	244.236	1.09083
	Squared	ns1-associated protein 1. [refseq;acc:nm_006372]	15043.7	18560.1	1.23375
	Rooted	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	50.7723	46.0607	1.10229
385	Measured	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	4533.74	5279.4	1.16447
	Ranked	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	266.421	244.236	1.09083
	Squared	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	15043.7	18560.1	1.23375
	Rooted	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	50.7723	46.0607	1.10229
386	Measured	60s ribosomal protein l8. [swissprot;acc:p25120]	4533.74	5279.4	1.16447
	Ranked	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	242.238	264.11	1.09029
	Squared	scratch; scratch 1. [refseq;acc:nm_031309]	40388.9	49827.5	1.23369
	Rooted	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	50.0513	45.4124	1.10215
387	Measured	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	4533.74	5279.4	1.16447
	Ranked	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	242.238	264.11	1.09029
	Squared	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	15053	18568	1.23351
	Rooted	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	50.3345	45.6718	1.10209
388	Measured	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	4533.74	5279.4	1.16447
	Ranked	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	227.575	208.756	1.09015

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.