Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

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Showing element 451 to 500 of 38536 in total

Network Comparison Type

: Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
29	Measured	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	0	111.278	High confidence	3.90833	434.911
	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	3121.28	Low confidence	1.19818	3739.84
	Ranked	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1	203.115	Low confidence	1.19089	170.557
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	7395	High confidence	1.57201	11625
		solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]	0	12129.6	Low confidence	1.39628	8687.07
		uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	1	187.458	High confidence	1.29991	243.678
	Squared	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	1	143.692	High confidence	3.18404	457.521
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	0	3.41692	Low confidence	9.62112	0.355148
		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	1	82347.8	Low confidence	1.33073	61881.5
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	5.18438	High confidence	27.2794	141.427
	Rooted	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	48.8531	Low confidence	1.16077	56.7071
		glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0	11.9583	Low confidence	1.7443	6.85565
		microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	0	17.7955	High confidence	2.42243	7.34614
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	26.0288	High confidence	1.65937	43.1914
30	Measured	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	1	36474.3	Low confidence	1.19288	43509.4
		dystrophin. [swissprot;acc:p11532]	0	427.217	High confidence	3.82335	111.739
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1	1834.59	High confidence	2.04837	895.633
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	0	105.5	Low confidence	2.97183	35.5
	Ranked	alpha 2 globin. [refseq;acc:nm_000517]	0	11486.2		1.39185	15987.1
		bcl2-related ovarian killer. [refseq;acc:nm_032515]	1	265.638		1.18995	223.235
		beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	7395	High confidence	1.57201	11625
		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	187.457		1.29991	243.678
	Squared	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]		143.692		3.18404	457.521
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0	3.41692	Low confidence	9.62112	0.355148
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	0	6.25494	High confidence	22.6931	141.944
	Rooted	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1	48.8781	Low confidence	1.16055	56.7253
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	26.0288	High confidence	1.65937	43.1914
		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]	0	13.0622	Low confidence	1.74163	7.5
		ptd016 protein. [refseq;acc:nm_016125]		5.47723	High confidence	2.29492	12.5698
31	Measured	dok-like protein. [refseq;acc:nm_024872]		35		3500000	0.00001
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1	1834.63		2.04827	895.697
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	0	105.5	Low confidence	2.97183	35.5
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	1	36469.3		1.19287	43503.3
	Ranked	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	1	57.395		1.17568	48.8186
		hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	0	11485.6		1.39168	15984.3
		leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	0	8082.33	High confidence	1.53462	5266.67
		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]	1	187.458		1.2999	243.677
	Squared	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	1	9924.76		2.53372	25146.6
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	5.54059		18.7211	103.726
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1	82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	0	3.41692		9.62112	0.355148
	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	145.551		1.1597	168.796
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	12.1655	High confidence	2.28539	27.8029
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	26.0288	High confidence	1.65937	43.1914
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	7.3589	Low confidence	1.73139	12.7411
32	Measured	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	598	High confidence	3.25	184
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	1	1834.73	High confidence	2.04793	895.893
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0	105.5	Low confidence	2.97183	35.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1	36360.3	Low confidence	1.19275	43368.8

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.

- http://analysis.yellowcouch.org/