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 2775 to 2824 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
347	scratch; scratch 1. [refseq;acc:nm_031309]	Rooted	0	21.5021	20.4389	1.05202
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Squared	1	16573.6	20637.8	1.24522
348	ad24 protein. [refseq;acc:nm_022451]	Rooted		49.2558	54.5235	1.10695
	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Ranked		242.14	265.696	1.09728
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Measured	0	14357.1	13463.1	1.0664
	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	Squared	1	42566.2	52985.3	1.24477
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Rooted		21.9882	20.9119	1.05147
	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	Measured	1	4991.02	5885.09	1.17914
349	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted	0	15.4361	14.7003	1.05005
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Measured		957.833	898.833	1.06564
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Measured	1	4714.85	5554.38	1.17806
	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	Squared		35533.9	44227	1.24464
	surfeit locus protein 5. [swissprot;acc:q15528]	Ranked		242.14	265.696	1.09728
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Rooted		56.0061	61.9704	1.10649
350	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	Squared		35508.7	44191.4	1.24452
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Rooted	0	38.0352	36.2234	1.05002
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured		48	51	1.0625
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Rooted	1	61.3383	67.8668	1.10643
	sedlin. [swissprot;acc:o14582]	Measured		17396.9	20483.9	1.17745
	zinc finger protein 291. [swissprot;acc:q9by12]	Ranked		242.14	265.696	1.09728
351	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	Rooted		61.3352	67.8618	1.10641
	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	Squared		35508.6	44191.3	1.24452
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured		48	51	1.0625
	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Ranked	1	242.14	265.696	1.09728
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Rooted	0	24.5101	25.7223	1.04946
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Measured	1	17396.9	20483.9	1.17745
352	40s ribosomal protein s28. [swissprot;acc:p25112]	Squared		30682.9	38183.6	1.24446
	bet3 homolog. [swissprot;acc:o43617]	Measured		17396.9	20483.9	1.17745
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	0	15.4896	14.7645	1.04911
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured		48	51	1.0625
	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Rooted	1	61.3354	67.8621	1.10641
	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	Ranked		242.14	265.696	1.09728
353	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	Squared		71383	57399.3	1.24362
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured	0	48	51	1.0625
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	mstp028 protein. [refseq;acc:nm_031954]	Rooted		64.9832	62.0398	1.04744
	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]		1	61.3354	67.8623	1.10641
	p66 alpha. [refseq;acc:nm_017660]	Measured		12839	10911.1	1.17669
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Ranked		231.73	211.252	1.09694

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.