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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	description	Network Comparison Type	green	Filtered	red	network_comparison
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]	Divided	434.911	0	111.278	3.90833
	Measured	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Subtracted	2399.76		3248.95	849.19
	Ranked	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		8257		13730.5	5473.5
		guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]		336.075	1	267.139	68.936
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Divided	11625	0	7395	1.57201
		uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]		243.678	1	187.458	1.29991
	Squared	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]		457.521	1	143.692	3.18404
		galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Subtracted	64272.5	0	72128.6	7856.1
		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]	Subtracted	129762	1	219048	89286
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided	141.427	0	5.18438	27.2794
	Rooted	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Subtracted	1.80368		11.3774	9.57372
		microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Divided	7.34614		17.7955	2.42243
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	43.1914	1	26.0288	1.65937
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	192.165	1	210.928	18.763
30	Measured	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Subtracted	4102.97	0	3265.25	837.72
		dystrophin. [swissprot;acc:p11532]	Divided	111.739	0	427.217	3.82335
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Divided	895.633	1	1834.59	2.04837
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Subtracted	18263	1	23693.7	5430.7
	Ranked	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Divided	11625	0	7395	1.57201
		guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Subtracted	336.075	1	267.14	68.935
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	8257	0	13730.5	5473.5
		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]	Divided	243.678	1	187.457	1.29991
	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]		457.521	1	143.692	3.18404
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		141.944	0	6.25494	22.6931
		segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	31089.6	0	23310.5	7779.1
		trophinin. [swissprot;acc:q12816]		129762	1	219048	89286
	Rooted	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		79.5099	1	60.8022	18.7077
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		9.43398	0	0	9.43398
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	43.1914	1	26.0288	1.65937
		ptd016 protein. [refseq;acc:nm_016125]		12.5698	0	5.47723	2.29492
31	Measured	dok-like protein. [refseq;acc:nm_024872]		0.00001	0	35	3500000
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		895.697	1	1834.63	2.04827
		melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Subtracted	18263	1	23693.7	5430.7
		spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]		2637	0	1833	804
	Ranked	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]		336.075	1	267.14	68.935
		leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Divided	5266.67	0	8082.33	1.53462
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Subtracted	6248	0	11627	5379
		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]	Divided	243.677	1	187.458	1.2999
	Squared	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	192141		106226	85915
		beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	25146.6		9924.76	2.53372
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Divided	103.726	0	5.54059	18.7211
		fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Subtracted	27772		35446.2	7674.2
	Rooted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	9.43398		0	9.43398
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided	27.8029		12.1655	2.28539
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	58.7986	1	40.0958	18.7028
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	43.1914	1	26.0288	1.65937
32	Measured	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]		184	0	598	3.25
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]		895.893	1	1834.73	2.04793
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	18263	1	23693.7	5430.7
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	58	0	859	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/