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 6662 to 6711 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
833	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	Ranked	Subtracted	229.171	238.048	8.877
	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	Rooted	Divided	59.7298	63.5169	1.0634
	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]	Measured		4489.72	4965.35	1.10594
834	60s ribosomal protein l8. [swissprot;acc:p25120]	Ranked		231.734	222.222	1.0428
	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	Measured		5623.18	6218.77	1.10592
	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Rooted		62.309	58.5957	1.06337
	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]	Squared	Subtracted	22335.8	26232.2	3896.4
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Measured		5929.55	6531.52	601.97
	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]	Ranked		230.768	239.632	8.864
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Squared	Divided	31100.2	36086.5	1.16033
	unr protein. [swissprot;acc:o75534]	Rooted	Subtracted	57.805	61.7803	3.9753
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	Measured	Divided	5623.18	6218.77	1.10592
	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Ranked		231.734	222.222	1.0428
	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]		Subtracted	224.413	233.272	8.859
	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Measured		5929.61	6531.55	601.94
	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]	Squared	Divided	31100.2	36086.5	1.16033
	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	Rooted	Subtracted	51.6042	55.574	3.9698
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]		Divided	120.033	112.905	1.06313
	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]	Squared	Subtracted	22335.8	26232.2	3896.4
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Measured	Divided	4049	4477.43	1.10581
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared		31100.2	36086.5	1.16033
	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	Rooted		65.0565	69.1533	1.06297
	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Ranked		231.734	222.222	1.0428
	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]	Rooted	Subtracted	51.6042	55.574	3.9698
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Squared		14247.4	18142.1	3894.7
	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	Ranked		224.413	233.272	8.859
	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	Measured		6229.69	6829.58	599.89
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]		Divided	4063.64	4492.98	1.10565
	down-regulated in metastasis. [refseq;acc:nm_014503]	Rooted	Subtracted	51.6042	55.574	3.9698
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared	Divided	31100.2	36086.5	1.16033
	kinesin family member c3. [refseq;acc:nm_005550]	Measured	Subtracted	5995.49	6595.35	599.86
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Ranked	Divided	231.734	222.222	1.0428
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Squared	Subtracted	14247.4	18142.1	3894.7
	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]	Ranked		237.62	228.762	8.858
	tubby protein homolog. [swissprot;acc:p50607]	Rooted	Divided	65.0565	69.1533	1.06297
838	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	Ranked	Subtracted	237.62	228.762	8.858
	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	Measured		6520.28	7119.28	599
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Squared	Divided	31100.1	36086.4	1.16033
	pbk1 protein. [sptrembl;acc:o76021]	Measured		4064.23	4493.36	1.10559
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	Rooted		65.0565	69.1533	1.06297
	rw1 protein (fragment). [swissprot;acc:q92545]	Ranked		231.734	222.222	1.0428
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Rooted	Subtracted	81.454	85.4078	3.9538
	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	Squared		22328.1	26222.3	3894.2
839	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	Measured	Divided	7093.86	7842.67	1.10556
	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]	Ranked	Subtracted	230.764	239.62	8.856
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Squared	Divided	31100.1	36086.4	1.16033
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Rooted		65.0565	69.1533	1.06297
	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]	Measured	Subtracted	6520.28	7119.28	599
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Ranked	Divided	177.776	170.499	1.04268
	target of myb protein 1. [swissprot;acc:o60784]	Rooted	Subtracted	61.6688	65.6175	3.9487

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.