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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	red	Filtered	green	network_comparison
29	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Rooted	Subtracted	11.3774	0	1.80368	9.57372
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared	Subtracted	72128.6	0	64272.5	7856.1
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Measured	Divided	1834.52	1	895.507	2.04858
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Ranked	Subtracted	267.139		336.075	68.936
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured		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		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	17.7955	0	7.34614	2.42243
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Ranked		7395		11625	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]	Measured		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		26.0288	1	43.1914	1.65937
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Rooted	Subtracted	210.928	1	192.165	18.763
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Measured	Subtracted	3248.95	0	2399.76	849.19
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Ranked	Divided	187.458	1	243.678	1.29991
30	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Ranked	Divided	7395	0	11625	1.57201
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted	3265.25	0	4102.97	837.72
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Rooted	Subtracted	60.8022	1	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	1	457.521	3.18404
	dystrophin. [swissprot;acc:p11532]	Measured		427.217	0	111.739	3.82335
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Measured		1834.59	1	895.633	2.04837
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Ranked	Subtracted	267.14	1	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	0	8257	5473.5
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured		23693.7	1	18263	5430.7
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted	Divided	26.0288	1	43.1914	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]	Squared		6.25494	0	141.944	22.6931
	ptd016 protein. [refseq;acc:nm_016125]	Rooted		5.47723		12.5698	2.29492
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Squared	Subtracted	23310.5		31089.6	7779.1
	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]	Ranked	Divided	187.457	1	243.678	1.29991
	trophinin. [swissprot;acc:q12816]	Squared	Subtracted	219048		129762	89286
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Subtracted	106226		192141	85915
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		Divided	9924.76		25146.6	2.53372
	dok-like protein. [refseq;acc:nm_024872]	Measured		35	0	0.00001	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]	Squared		5.54059		103.726	18.7211
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Squared	Subtracted	35446.2		27772	7674.2
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Measured	Divided	1834.63	1	895.697	2.04827
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Ranked	Subtracted	267.14	1	336.075	68.935
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Rooted	Subtracted	0	0	9.43398	9.43398
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Ranked	Divided	8082.33	0	5266.67	1.53462
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Measured	Subtracted	23693.7	1	18263	5430.7
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Ranked	Subtracted	11627	0	6248	5379
		Rooted	Divided	12.1655	0	27.8029	2.28539
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		Subtracted	40.0958	1	58.7986	18.7028
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Divided	26.0288		43.1914	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]	Ranked	Divided	187.458		243.677	1.2999
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Measured	Subtracted	1833	0	2637	804
32	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared	Divided	9924.76	1	25146.6	2.53372
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Measured		598	0	184	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]	Rooted		26.0288	1	43.1914	1.65937
	gbp protein isoform a. [refseq;acc:nm_017870]	Rooted	Subtracted	23.9771	1	42.4773	18.5002

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/