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 741 to 790 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
93	Squared	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	1	29567	18601.6	1.58949
		myosin vi. [swissprot;acc:q9um54]	0	39.56	17.2035	2.29953
	Rooted	cab2. [refseq;acc:nm_033419]		0.00001	13.1909	1319090
		cullin homolog 1 (cul-1). [swissprot;acc:q13616]	1	37.3005	48.4141	1.29795
94	Measured	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		4247.86	5941.88	1.39879
		myosin vi. [swissprot;acc:q9um54]	0	345.865	224.096	1.54338
	Ranked	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1	88.2482	110.265	1.24949
		transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	0	12946.3	10519.7	1.23067
	Squared	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]		122.543	53.9854	2.26993
		ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	1	84857.8	53402.4	1.58903
	Rooted	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]		47.6504	36.9304	1.29028
		hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	0	24.7769	18.7862	1.31889
95	Measured	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154	0.00001	15400000
		son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1	2397.19	3343.62	1.39481
	Ranked	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		88.2482	110.265	1.24949
		pp3111 protein. [refseq;acc:nm_022156]	0	6185	7603	1.22926
	Squared	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	1	256169	162517	1.57626
		transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	0	631.532	280.389	2.25234
	Rooted	metaxin 1. [swissprot;acc:q13505]		14.7289	11.2174	1.31304
		regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	1	47.6504	36.9304	1.29028
96	Measured	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		4110.14	5694.99	1.3856
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	154	0.00001	15400000
	Ranked	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]		8335.82	10228.3	1.22703
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	1	88.2482	110.265	1.24949
	Squared	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		7744.68	4959.41	1.56161
		glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	0	52.0821	116.513	2.2371
	Rooted	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	1	47.6504	36.9304	1.29028
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	65.4535	49.8523	1.31295
97	Measured	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]		728.65	476.619	1.52879
		amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	1	2820.51	3897.1	1.3817
	Ranked	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		88.2482	110.265	1.24949
		microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	0	8335.82	10228.3	1.22703
	Squared	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	1	227160	146079	1.55505
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	0	10489.8	23426.5	2.23326
	Rooted	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	1	47.6504	36.9304	1.29028
		ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	0	13.2903	17.4395	1.3122
98	Measured	pp3111 protein. [refseq;acc:nm_022156]		789	530	1.48868
		presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	1	2353.63	3225.65	1.3705
	Ranked	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		88.2482	110.265	1.24949
		orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	0	7234.6	8858.94	1.22452
	Squared	pp3111 protein. [refseq;acc:nm_022156]		147.342	66.4852	2.21616
		trs85 homolog. [swissprot;acc:q9y2l5]	1	227160	146079	1.55505
	Rooted	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	0	13.2903	17.4395	1.3122
		transcription factor lbx1. [swissprot;acc:p52954]	1	47.6504	36.9304	1.29028
99	Measured	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]		2353.63	3225.65	1.3705
		transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	0	817.81	551.434	1.48306
	Ranked	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1	88.2482	110.265	1.24949
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	0	12787.8	10454.7	1.22316
	Squared	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]		492.157	225.924	2.17842
		wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	1	226186	145568	1.55382

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.