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

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	Interaction Map	Filtered	red	green	network_comparison

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Showing element 4758 to 4807 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
298	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted	Subtracted	0	15.6205	13.9284	1.6921
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Measured			2131.83	2218.82	86.99
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Squared		1	28901.4	36762.1	7860.7
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]		Divided	0	1775.39	1465.73	1.21127
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Rooted	Subtracted	1	66.1064	74.1073	8.0009
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Ranked		0	19713.5	18962.5	751
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Squared	Divided	1	14247.4	18142.1	1.27336
	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]	Rooted			57.6823	64.4212	1.11683
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Ranked	Subtracted		266.421	244.236	22.185
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Measured	Divided		4633.92	5572.85	1.20262
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]			0	939	848	1.10731
299	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	Ranked			12338.7	11512.3	1.07178
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Measured		1	4914.27	5907.12	1.20203
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Ranked			268.635	243.592	1.10281
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Squared	Subtracted		51527.6	43689.1	7838.5
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Measured	Divided	0	2231.05	2015.09	1.10717
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared	Subtracted		166.774	90.363	76.411
	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	Rooted		1	66.1063	74.1068	8.0005
	histone h2b. [refseq;acc:nm_175055]	Measured		0	2131.91	2218.89	86.98
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Rooted	Divided		19.4501	18.1126	1.07384
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Ranked	Subtracted		10194.1	10941.8	747.7
	metaxin 1. [swissprot;acc:q13505]	Measured		1	9327.58	10442.2	1114.62
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Rooted		0	7.7419	6.06104	1.68086
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Squared	Divided	1	28896.2	36767	1.27238
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Rooted			59.026	65.8955	1.11638
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Squared		0	618.307	511.996	1.20764
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked	Subtracted	1	266.421	244.236	22.185
300	60s ribosomal protein l15. [swissprot;acc:p39030]	Squared		0	1362.84	1286.61	76.23
	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	Ranked	Divided		9270.49	8650.24	1.0717
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Squared			65.2367	78.5269	1.20372
	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]		Subtracted	1	51527.6	43689.1	7838.5
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Rooted			43.5479	51.5473	7.9994
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Measured		0	2131.93	2218.9	86.97
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked			16321	15577	744
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]		Divided	1	150.959	166.351	1.10196
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Rooted			48.1584	53.7378	1.11586
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]			0	93.6109	87.2238	1.07323
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Ranked	Subtracted	1	257.017	234.945	22.072
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted		0	13.6748	12	1.6748
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Measured	Divided		1334.19	1205.1	1.10712
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]		Subtracted	1	4446.72	5553.79	1107.07
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Squared	Divided		28896.2	36767	1.27238
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Measured			4914.27	5907.12	1.20203
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Ranked			150.982	166.372	1.10193
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Rooted	Subtracted		66.1048	74.0977	7.9929
	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]	Squared			51527.6	43689.1	7838.5
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Measured	Divided		13768.2	11466	1.20078
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Rooted		0	12.7534	11.8854	1.07303
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Measured			135.294	149.371	1.10405
	histone h2b.c (h2b/c). [swissprot;acc:q99880]		Subtracted		2132.04	2218.98	86.94

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.