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 5908 to 5957 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
370	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Measured	Subtracted	0	320.752	368.317	47.565
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]		Divided		1049.21	989.438	1.06041
	grancalcin. [swissprot;acc:p28676]	Squared	Subtracted	1	29095.7	35338.3	6242.6
	grb2-related adaptor protein. [swissprot;acc:q13588]	Rooted			61.4282	68.0107	6.5825
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Measured	Divided		4108.15	4808.93	1.17058
	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]	Rooted			49.7435	45.0586	1.10397
	mstp028 protein. [refseq;acc:nm_031954]	Ranked	Subtracted	0	7965.66	7528.21	437.45
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]			1	218.818	238.358	19.54
	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	Measured			7753.59	8728.13	974.54
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Ranked	Divided		242.159	265.104	1.09475
	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	Squared			45986	56776.1	1.23464
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Ranked		0	13652.7	13061	1.0453
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Squared			1039.56	927.649	1.12064
371	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Measured	Subtracted		884.254	931.405	47.151
	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]	Squared	Divided	1	45985.9	56776	1.23464
	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]		Subtracted		29095.3	35337.6	6242.3
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]		Divided	0	18585	20796.3	1.11898
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Rooted	Subtracted		30.454	29.4181	1.0359
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Squared			47.4746	74.0536	26.579
	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	6.5285
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Ranked			186.172	166.661	19.511
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Measured	Divided	0	1631.97	1542.23	1.05819
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]		Subtracted	1	4855.46	5824.52	969.06
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Rooted	Divided	0	20.9428	21.8063	1.04123
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Ranked		1	186.52	170.42	1.09447
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Measured			5067.02	5926.46	1.16961
	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]	Ranked		0	13247.9	12674.2	1.04527
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]		Subtracted		12576	13010	434
	zinc finger-like protein 9. [refseq;acc:nm_033414]	Rooted	Divided	1	49.3451	54.4606	1.10367
372	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	Squared			45986.7	56776.8	1.23464
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Ranked	Subtracted	0	8356.31	8788.62	432.31
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Measured	Divided		5427.25	5130.58	1.05782
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Ranked			11869.9	12402.7	1.04489
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Squared			21.836	19.5177	1.11878
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Measured	Subtracted		3693.07	3739.55	46.48
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Rooted			29.6492	28.6255	1.0237
	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]		Divided	1	49.3451	54.4606	1.10367
	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]		Subtracted		61.3354	67.8623	6.5269
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Ranked			239.709	259.038	19.329
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Squared			29335.6	35515.5	6179.9
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Measured	Divided		5067	5926.17	1.16956
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Ranked			186.52	170.42	1.09447
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Rooted		0	11.9476	12.4394	1.04116
	serpin b12. [swissprot;acc:q96p63]	Squared	Subtracted		23.5744	0.0289898	23.5454
	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	969
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	Ranked	Divided		242.37	265.255	1.09442
	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Squared	Subtracted		28863.2	35031.5	6168.3
	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]		Divided		45986	56776.1	1.23464
	dynactin 4. [refseq;acc:nm_032486]	Ranked	Subtracted		233.142	252.253	19.111
	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	Rooted	Divided		49.3451	54.4606	1.10367

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.