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

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Showing element 2801 to 2850 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
1401	ATF2	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	Divided	218.657	214.11	1.02124
	NR6A1	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Subtracted	212.833	208.456	4.377
1402	MCC	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	Divided	209.682	205.329	1.0212
			Subtracted			4.353
1403	CPSF2	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]		110.2	114.552	4.352
	ECHS1	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Divided	184.656	180.823	1.0212
1404	KRR1	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	Subtracted	242.181	237.834	4.347
	SF3B4	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	Divided	232.752	237.65	1.02104
1405	EIF3C	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]		245.532	240.483	1.021
	EVI5L	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	Subtracted	218.829	214.493	4.336
1406	EVI5	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
	NR6A1	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Divided	212.833	208.456	1.021
1407	WDFY1	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]		206.104	210.424	1.02096
			Subtracted			4.32
1408	STIM1	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	Divided	206.102	210.42	1.02095
			Subtracted			4.318
1409	MED30	trap/mediator complex component trap25. [refseq;acc:nm_080651]	Divided			1.02095
			Subtracted			4.318
1410	PAK4	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]
	WDFY2	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	Divided	206.1	210.417	1.02095
1411	PAK4	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]		206.102	210.42
	REEP5	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Subtracted			4.318
1412	ACADM	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
	REEP5	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Divided			1.02095
1413	ACADM	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
	REEP6	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Subtracted			4.318
1414			Divided			1.02095
	STIM2	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	Subtracted			4.318
1415	PAK7	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
	STIM2	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	Divided			1.02095
1416	PAK7	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
	WDFY2	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	Subtracted	206.1	210.417	4.317
1417	ASAH1	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]		207.076	211.391	4.315
	CPA5	carboxypeptidase a5. [refseq;acc:nm_080385]	Divided	203.979	208.229	1.02084
1418	CPB1	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
	CRX	cone-rod homeobox protein. [swissprot;acc:o43186]	Subtracted	244.331	240.061	4.27
1419	OTX1	homeobox protein otx1. [swissprot;acc:p32242]		244.367	240.098	4.269
	SLC3A1	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	Divided	203.979	208.229	1.02084
1420	ACY1	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
	OTX2	homeobox protein otx2. [swissprot;acc:p32243]	Subtracted	244.478	240.212	4.266
1421	ASAH1	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	Divided	207.076	211.391	1.02084
	CPA5	carboxypeptidase a5. [refseq;acc:nm_080385]	Subtracted	203.979	208.229	4.25
1422	CPA1	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	Divided			1.02084
	CPB1	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]	Subtracted			4.25
1423	no value	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	Divided	221.152	216.659	1.02074
	SLC3A1	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	Subtracted	203.979	208.229	4.25
1424	ACY1	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
	ATP1A1	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	Divided	214.717	219.157	1.02068
1425	CPA1	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	Subtracted	203.979	208.229	4.25
	CTSL2	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	Divided	214.717	219.157	1.02068

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
- Hugo is the HGNC identifier if it exists
- 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.