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 4608 to 4657 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
288	syntaxin 10 (syn10). [swissprot;acc:o60499]	Ranked	Subtracted	1	234.691	257.442	22.751
289	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]			0	10614.2	9812.39	801.81
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Rooted			22.6917	24.5013	1.8096
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	Divided		5868.74	4797.35	1.22333
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Rooted			28.6008	30.8974	1.0803
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Ranked			15147.2	14091.9	1.07489
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Measured	Subtracted	1	4069.83	5252.17	1182.34
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			0	0	89	89
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Ranked	Divided	1	272.781	246.892	1.10486
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Squared			6693.64	8564.94	1.27956
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Rooted			57.4274	64.2609	1.11899
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	Subtracted	0	207.597	118.463	89.134
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Rooted		1	55.8956	63.9636	8.068
	syntaxin 6. [swissprot;acc:o43752]	Ranked			234.673	257.414	22.741
	tubby protein homolog. [swissprot;acc:p50607]	Measured	Divided	0	3797.57	4228.27	1.11341
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Squared	Subtracted	1	28896.2	36767	7870.8
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Measured	Divided		4682.88	5646.19	1.20571
290	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Squared			15734.4	20126.8	1.27916
	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Rooted	Subtracted	0	45.8794	47.6722	1.7928
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		Divided	1	75.6323	67.6572	1.11788
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]			0	22.6917	24.5013	1.07975
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Measured			1370.82	1525.56	1.11288
	dystrophin. [swissprot;acc:p11532]	Squared	Subtracted		98.4011	12.5624	85.8387
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Measured		1	4071.1	5251.75	1180.65
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]			0	0	89	89
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Squared	Divided		6188.69	7568.12	1.2229
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Ranked			15147.2	14091.9	1.07489
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared	Subtracted	1	28896.2	36767	7870.8
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Ranked	Divided		231.969	210.064	1.10428
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]		Subtracted	0	3474	2695	779
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]			1	242.109	264.79	22.681
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Measured	Divided		4991.48	6014.08	1.20487
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Rooted	Subtracted		66.1122	74.1438	8.0316
291	60s ribosomal protein l39. [swissprot;acc:p02404]	Squared		0	10474.5	10558.6	84.1
	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	Ranked		1	241.509	264.163	22.654
	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]		Divided	0	10922.9	11731.8	1.07406
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Rooted	Subtracted		5.01247	6.80523	1.79276
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured			0	89	89
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Ranked			11414.1	12191.8	777.7
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]		Divided	1	251.679	228.037	1.10368
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Measured	Subtracted		5894.75	7073.65	1178.9
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Rooted			66.1064	74.1074	8.001
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured	Divided		44490.5	36927.5	1.20481
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]			0	1961.09	2179.77	1.11151
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Rooted			136.763	147.411	1.07786
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	Squared			1021.12	1246	1.22023
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]			1	59016.1	75486.9	1.27909
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]		Subtracted		28896.2	36767	7870.8
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Rooted	Divided		113.983	101.979	1.11771
292	40s ribosomal protein s15a. [swissprot;acc:p39027]	Ranked			241.411	266.414	1.10357

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.