MK5 Microarray Data

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 2480 to 2529 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
310	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Measured	1	4909.79	5878.79	1.19736
311	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	Squared		30566.4	38866.5	1.27154
	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked	0	10253.5	9622.45	1.06558
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Squared		1326.34	1126.71	1.17718
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Rooted	1	95.0526	85.3206	1.11406
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Ranked		242.627	267.151	1.10108
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured		4981.52	5964.58	1.19734
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Rooted	0	31.7744	33.8609	1.06567
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Measured		3117.17	2833.94	1.09994
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Ranked	1	242.195	266.663	1.10103
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Rooted	0	25.2821	26.9306	1.0652
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Measured		3455.43	3800.29	1.0998
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked		11959.8	12731.1	1.06449
	methyltransferase like 2. [refseq;acc:nm_018396]	Squared	1	71576.8	56326.7	1.27074
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Rooted		95.0526	85.3206	1.11406
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Measured		4598.21	5500.48	1.19622
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Squared	0	25325.5	29804.9	1.17687
313	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Measured		6131.07	6739.34	1.09921
	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Squared	1	71576.8	56326.7	1.27074
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	Rooted	0	25.2821	26.9306	1.0652
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked		11935.6	12698.9	1.06395
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Rooted	1	95.0526	85.3206	1.11406
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Measured		21644.2	18098.7	1.1959
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Ranked		232.473	211.207	1.10069
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Squared	0	25325.5	29804.9	1.17687
314	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Ranked		10301.4	10957.5	1.06369
	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Squared	1	71576.8	56326.7	1.27074
	kappa b-ras 1. [refseq;acc:nm_020345]	Rooted	0	21.0189	22.3788	1.0647
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Ranked	1	244.126	268.604	1.10027
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Rooted		95.0526	85.3206	1.11406
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Squared	0	6027.87	7086.08	1.17555
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Measured	1	21632.5	18090	1.19583
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]		0	5302.7	4827.7	1.09839
315	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]			1212.82	1104.61	1.09796
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Rooted		17.9172	16.833	1.06441
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared		36059.4	30745.3	1.17284
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Ranked	1	244.126	268.604	1.10027
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Rooted		95.0526	85.3206	1.11406
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Squared		71576.8	56326.7	1.27074
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Ranked	0	12121.6	12887.6	1.06319
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Measured	1	21370.8	17896.5	1.19413
316	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Squared	0	8620.27	7355.46	1.17196
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Measured		525	576	1.09714
	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Ranked		10768.5	11444	1.06273
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Rooted	1	95.0526	85.3206	1.11406
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Squared		28918.3	36746	1.27068
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Ranked		242.694	267.017	1.10022
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Measured		21370.8	17896.5	1.19413
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Rooted	0	41.4068	38.9073	1.06424
317	adiponectin receptor 2. [refseq;acc:nm_024551]	Measured	1	3153.1	3762.56	1.19329

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.