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

Results: HTML CSV LaTeX

Showing element 901 to 950 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
29	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Rooted	Subtracted	High confidence	0	11.3774	1.80368	9.57372
	cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954]	Measured		Low confidence	0	20505.7	21088.5	582.8
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Squared			1	92930.5	71802.4	21128.1
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Rooted	Divided		1	48.8531	56.7071	1.16077
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared	Subtracted	High confidence	0	72128.6	64272.5	7856.1
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Ranked	Subtracted	Low confidence		11761	15924	4163
		Rooted	Divided	Low confidence		11.9583	6.85565	1.7443
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Measured	Divided	High confidence	1	1834.52	895.507	2.04858
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Ranked	Subtracted	High confidence	1	267.139	336.075	68.936
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared	Divided	Low confidence	0	3.41692	0.355148	9.62112
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared			1	82347.8	61881.5	1.33073
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured			0	105.5	35.5	2.97183
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	Subtracted	High confidence	1	23693.7	18263	5430.7
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Squared	Subtracted		1	219048	129762	89286
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Rooted	Divided		0	17.7955	7.34614	2.42243
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Ranked	Divided			7395	11625	1.57201
	pnas-129. [sptrembl;acc:q9bxv8]	Rooted	Subtracted	Low confidence		16.4276	9.246	7.1816
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Divided	High confidence		111.278	434.911	3.90833
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Squared				5.18438	141.427	27.2794
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Rooted			1	26.0288	43.1914	1.65937
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Rooted	Subtracted		1	210.928	192.165	18.763
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Measured			0	3248.95	2399.76	849.19
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Rooted		Low confidence	1	76.5734	88.6244	12.051
	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured			1	13081.2	14872.6	1791.4
	solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]	Ranked	Divided		0	12129.6	8687.07	1.39628
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	Subtracted		0	8202.27	15317.3	7115.03
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	Divided		1	3121.28	3739.84	1.19818
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Ranked		High confidence	1	187.458	243.678	1.29991
30	alpha 2 globin. [refseq;acc:nm_000517]			Low confidence	0	11486.2	15987.1	1.39185
	bcl2-related ovarian killer. [refseq;acc:nm_032515]				1	265.638	223.235	1.18995
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Measured			1	36474.3	43509.4	1.19288
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Ranked		High confidence	0	7395	11625	1.57201
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted		0	3265.25	4102.97	837.72
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Rooted	Subtracted		1	60.8022	79.5099	18.7077
	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]	Squared	Divided			143.692	457.521	3.18404
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Rooted		Low confidence		48.8781	56.7253	1.16055
	dystrophin. [swissprot;acc:p11532]	Measured		High confidence	0	427.217	111.739	3.82335
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Measured			1	1834.59	895.633	2.04837
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Ranked	Subtracted		1	267.14	336.075	68.935
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Rooted			0	0	9.43398	9.43398
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Ranked				13730.5	8257	5473.5
		Squared		Low confidence		1082.48	7964.87	6882.39
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Squared			1	92930	71802.1	21127.9
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured	Divided		0	105.5	35.5	2.97183
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared			1	82347.8	61881.5	1.33073
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared			0	3.41692	0.355148	9.62112
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	Subtracted	High confidence	1	23693.7	18263	5430.7
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted	Divided	High confidence		26.0288	43.1914	1.65937
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Measured	Subtracted	Low confidence		3278	5058.5	1780.5
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Squared	Divided	High confidence	0	6.25494	141.944	22.6931

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/