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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	Network Comparison Type	description	red	green	Filtered	network_comparison
29	Measured	Subtracted	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	23693.7	18263	1	5430.7
	Measured	Subtracted	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	3248.95	2399.76	0	849.19
	Ranked	Divided	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	7395	11625	0	1.57201
		Divided	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	187.458	243.678	1	1.29991
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	13730.5	8257	0	5473.5
		Subtracted	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	267.139	336.075	1	68.936
	Squared	Divided	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	143.692	457.521	1	3.18404
		Divided	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	5.18438	141.427	0	27.2794
		Subtracted	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	72128.6	64272.5	0	7856.1
		Subtracted	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]	219048	129762	1	89286
	Rooted	Divided	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	17.7955	7.34614	0	2.42243
		Divided	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	26.0288	43.1914	1	1.65937
		Subtracted	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	11.3774	1.80368	0	9.57372
		Subtracted	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	210.928	192.165	1	18.763
30	Measured	Divided	dystrophin. [swissprot;acc:p11532]	427.217	111.739	0	3.82335
		Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1834.59	895.633	1	2.04837
		Subtracted	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	3265.25	4102.97	0	837.72
		Subtracted	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	23693.7	18263	1	5430.7
	Ranked	Divided	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	7395	11625	0	1.57201
		Divided	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]	187.457	243.678	1	1.29991
		Subtracted	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	267.14	336.075	1	68.935
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	13730.5	8257	0	5473.5
	Squared	Divided	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	457.521	1	3.18404
		Divided	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	6.25494	141.944	0	22.6931
		Subtracted	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	23310.5	31089.6	0	7779.1
		Subtracted	trophinin. [swissprot;acc:q12816]	219048	129762	1	89286
	Rooted	Divided	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	26.0288	43.1914	1	1.65937
		Divided	ptd016 protein. [refseq;acc:nm_016125]	5.47723	12.5698	0	2.29492
		Subtracted	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	60.8022	79.5099	1	18.7077
		Subtracted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	9.43398	0	9.43398
31	Measured	Divided	dok-like protein. [refseq;acc:nm_024872]	35	0.00001	0	3500000
		Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	1834.63	895.697	1	2.04827
		Subtracted	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	23693.7	18263	1	5430.7
		Subtracted	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	1833	2637	0	804
	Ranked	Divided	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	8082.33	5266.67	0	1.53462
		Divided	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]	187.458	243.677	1	1.2999
		Subtracted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	267.14	336.075	1	68.935
		Subtracted	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	11627	6248	0	5379
	Squared	Divided	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	9924.76	25146.6	1	2.53372
		Divided	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	5.54059	103.726	0	18.7211
		Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	106226	192141	1	85915
		Subtracted	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	35446.2	27772	0	7674.2
	Rooted	Divided	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	12.1655	27.8029	0	2.28539
		Divided	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	26.0288	43.1914	1	1.65937
		Subtracted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	9.43398	0	9.43398
		Subtracted	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	40.0958	58.7986	1	18.7028
32	Measured	Divided	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	598	184	0	3.25
		Divided	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	1834.73	895.893	1	2.04793
		Subtracted	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	23693.7	18263	1	5430.7
		Subtracted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	58	0	801

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/