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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Filtered	green	Value Type	Interaction Map	red	network_comparison
29	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	56.7071	Rooted	Low confidence	48.8531	1.16077
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0	6.85565			11.9583	1.7443
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	895.507	Measured	High confidence	1834.52	2.04858
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	0	0.355148	Squared	Low confidence	3.41692	9.62112
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	1	61881.5			82347.8	1.33073
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	35.5	Measured		105.5	2.97183
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]		7.34614	Rooted	High confidence	17.7955	2.42243
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		11625	Ranked		7395	1.57201
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		434.911	Measured		111.278	3.90833
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]		141.427	Squared		5.18438	27.2794
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	43.1914	Rooted		26.0288	1.65937
	solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]	0	8687.07	Ranked	Low confidence	12129.6	1.39628
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	3739.84	Measured		3121.28	1.19818
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]		243.678	Ranked	High confidence	187.458	1.29991
30	alpha 2 globin. [refseq;acc:nm_000517]	0	15987.1		Low confidence	11486.2	1.39185
	bcl2-related ovarian killer. [refseq;acc:nm_032515]	1	223.235			265.638	1.18995
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		43509.4	Measured		36474.3	1.19288
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	11625	Ranked	High confidence	7395	1.57201
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	1	457.521	Squared		143.692	3.18404
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		56.7253	Rooted	Low confidence	48.8781	1.16055
	dystrophin. [swissprot;acc:p11532]	0	111.739	Measured	High confidence	427.217	3.82335
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1	895.633			1834.59	2.04837
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	0	35.5		Low confidence	105.5	2.97183
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1	61881.5	Squared		82347.8	1.33073
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0	0.355148			3.41692	9.62112
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	43.1914	Rooted	High confidence	26.0288	1.65937
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	0	141.944	Squared		6.25494	22.6931
	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]		7.5	Rooted	Low confidence	13.0622	1.74163
	ptd016 protein. [refseq;acc:nm_016125]		12.5698		High confidence	5.47723	2.29492
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	1	243.678	Ranked		187.457	1.29991
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		168.796	Rooted	Low confidence	145.551	1.1597
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		25146.6	Squared	High confidence	9924.76	2.53372
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]		48.8186	Ranked	Low confidence	57.395	1.17568
	dok-like protein. [refseq;acc:nm_024872]	0	0.00001	Measured	High confidence	35	3500000
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]		103.726	Squared		5.54059	18.7211
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1	895.697	Measured		1834.63	2.04827
	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	0	15984.3	Ranked	Low confidence	11485.6	1.39168
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]		35.5	Measured		105.5	2.97183
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]		5266.67	Ranked	High confidence	8082.33	1.53462
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1	61881.5	Squared	Low confidence	82347.8	1.33073
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	0	0.355148			3.41692	9.62112
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]		27.8029	Rooted	High confidence	12.1655	2.28539
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	43.1914			26.0288	1.65937
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]		243.677	Ranked		187.458	1.2999
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	12.7411	Rooted	Low confidence	7.3589	1.73139
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	1	43503.3	Measured		36469.3	1.19287
32	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		25146.6	Squared	High confidence	9924.76	2.53372
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	184	Measured		598	3.25
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	43.1914	Rooted		26.0288	1.65937
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]		895.893	Measured		1834.73	2.04793

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.