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

Results: HTML CSV LaTeX

Showing element 3758 to 3807 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
470	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Rooted	1	60.0148	65.6429	1.09378
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	Rooted	0	18.7853	18.9683	1.00974
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Squared	1	10418.3	8641.84	1.20557
471	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Ranked	0	11319.2	11463	1.0127
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Ranked	1	248.152	267.226	1.07686
	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	Measured		9649.61	11053.5	1.14549
	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]	Squared		28188.7	33982.7	1.20554
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Rooted	0	93.5322	92.7071	1.0089
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Squared		6607.52	6525.61	1.01255
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Measured		3855.78	3825.73	1.00785
	vav-2 protein. [swissprot;acc:p52735]	Rooted	1	66.088	72.2597	1.09339
472	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Squared	0	6605.9	6524	1.01255
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Rooted	0	110.816	111.772	1.00863
	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]	Squared	1	28190.4	33984.1	1.20552
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Measured	0	3889.5	3919.25	1.00765
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Ranked	0	7080.27	7165.6	1.01205
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Measured	1	9649.61	11053.5	1.14549
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Ranked		248.152	267.226	1.07686
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Rooted		50.3767	46.0753	1.09336
473	40s ribosomal protein s3a. [swissprot;acc:p49241]	Squared	0	8653.02	8550.86	1.01195
	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	Squared	1	28190.4	33984.1	1.20552
	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	Ranked	0	816	825	1.01103
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Measured		3889.5	3919.25	1.00765
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Rooted		110.861	111.817	1.00862
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Ranked	1	225.661	209.651	1.07637
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Rooted		62.574	68.4128	1.09331
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Measured		9649.61	11053.5	1.14549
474	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Measured	0	2281.12	2263.85	1.00763
	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]	Squared	1	28190.4	33984.1	1.20552
	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]	Rooted	1	62.574	68.4128	1.09331
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Rooted	0	110.799	111.754	1.00862
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Squared		58677.8	58207.8	1.00807
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Ranked		11290.1	11167.6	1.01097
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	Ranked	1	226.789	210.818	1.07576
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Measured	1	9649.61	11053.5	1.14549
475	60s ribosomal protein l18a. [swissprot;acc:q02543]	Squared	0	9310.69	9385.52	1.00804
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Ranked		18667	18500	1.00903
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Measured		2319.24	2335.98	1.00722
	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]	Rooted	1	62.574	68.4128	1.09331
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	Measured	1	9649.61	11053.5	1.14549
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Rooted	0	110.625	111.576	1.0086
	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]	Squared	1	28192	33985.3	1.20549
	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	Ranked	1	226.727	210.816	1.07547
476	60s ribosomal protein l39. [swissprot;acc:p02404]	Squared	0	10474.5	10558.6	1.00803
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked		8403	8329	1.00888
	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	Measured		1362.55	1372.31	1.00716
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Rooted		110.543	111.493	1.00859
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Measured	1	9649.61	11053.5	1.14549
	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	Ranked		226.681	210.814	1.07527
	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]	Rooted		62.574	68.4128	1.09331

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/