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

Results: HTML CSV LaTeX

Showing element 451 to 500 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	green	network_comparison	red
29	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Rooted	Subtracted	0	1.80368	9.57372	11.3774
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared	Subtracted	0	64272.5	7856.1	72128.6
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Measured	Divided	1	895.507	2.04858	1834.52
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Ranked	Subtracted		336.075	68.936	267.139
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured			18263	5430.7	23693.7
	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			129762	89286	219048
	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	7.34614	2.42243	17.7955
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Ranked			11625	1.57201	7395
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured			434.911	3.90833	111.278
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Squared			141.427	27.2794	5.18438
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Rooted		1	43.1914	1.65937	26.0288
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Rooted	Subtracted	1	192.165	18.763	210.928
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Measured	Subtracted	0	2399.76	849.19	3248.95
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Ranked	Divided	1	243.678	1.29991	187.458
30	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Ranked	Divided	0	11625	1.57201	7395
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted	0	4102.97	837.72	3265.25
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Rooted	Subtracted	1	79.5099	18.7077	60.8022
	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	1	457.521	3.18404	143.692
	dystrophin. [swissprot;acc:p11532]	Measured		0	111.739	3.82335	427.217
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Measured		1	895.633	2.04837	1834.59
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Ranked	Subtracted	1	336.075	68.935	267.14
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Rooted		0	9.43398	9.43398	0
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Ranked		0	8257	5473.5	13730.5
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured		1	18263	5430.7	23693.7
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted	Divided	1	43.1914	1.65937	26.0288
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Squared		0	141.944	22.6931	6.25494
	ptd016 protein. [refseq;acc:nm_016125]	Rooted			12.5698	2.29492	5.47723
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Squared	Subtracted		31089.6	7779.1	23310.5
	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]	Ranked	Divided	1	243.678	1.29991	187.457
	trophinin. [swissprot;acc:q12816]	Squared	Subtracted		129762	89286	219048
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Subtracted		192141	85915	106226
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		Divided		25146.6	2.53372	9924.76
	dok-like protein. [refseq;acc:nm_024872]	Measured		0	0.00001	3500000	35
	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			103.726	18.7211	5.54059
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Squared	Subtracted		27772	7674.2	35446.2
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Measured	Divided	1	895.697	2.04827	1834.63
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Ranked	Subtracted	1	336.075	68.935	267.14
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Rooted	Subtracted	0	9.43398	9.43398	0
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Ranked	Divided	0	5266.67	1.53462	8082.33
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Measured	Subtracted	1	18263	5430.7	23693.7
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Ranked	Subtracted	0	6248	5379	11627
		Rooted	Divided	0	27.8029	2.28539	12.1655
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		Subtracted	1	58.7986	18.7028	40.0958
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Divided		43.1914	1.65937	26.0288
	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		243.677	1.2999	187.458
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Measured	Subtracted	0	2637	804	1833
32	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared	Divided	1	25146.6	2.53372	9924.76
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Measured		0	184	3.25	598
	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		1	43.1914	1.65937	26.0288
	gbp protein isoform a. [refseq;acc:nm_017870]	Rooted	Subtracted	1	42.4773	18.5002	23.9771

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/