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

Results: HTML CSV LaTeX

Showing element 5358 to 5407 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
335	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Ranked	Subtracted	0	10897	11520	623
	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	Squared	Divided	1	30651.3	38253.3	1.24802
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Measured	Subtracted		1631.67	2664.55	1032.88
336	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Squared		0	44.3683	0.344399	44.0239
	60s ribosomal protein l11. [swissprot;acc:p39026]	Rooted	Divided	1	50.3167	45.4063	1.10814
	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	Squared	Subtracted		36109.8	42811.6	6701.8
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Rooted	Divided	0	20.5317	19.4823	1.05386
	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	Ranked	Subtracted		9270.49	8650.24	620.25
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]		Divided	1	312	284	1.09859
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Measured		0	1766.66	1908.13	1.08008
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]			1	3751.3	4431.34	1.18128
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Squared			46785.7	58383.2	1.24789
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]			0	3680.43	3222.6	1.14207
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Measured	Subtracted	1	1631.67	2664.55	1032.88
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Rooted		0	9.27362	8	1.27362
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Ranked	Divided		8125.5	7697.5	1.0556
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Rooted	Subtracted	1	59.4073	66.7002	7.2929
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Measured		0	2070.81	2134.56	63.75
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Ranked		1	241.045	261.874	20.829
337	60s ribosomal protein l12. [swissprot;acc:p30050]		Divided		243.583	267.527	1.0983
	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Measured		0	2039.07	2194.52	1.07624
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Rooted		1	77.5801	70.0182	1.108
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]			0	56.92	59.965	1.0535
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Ranked			12953.2	12273.2	1.05541
	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Squared	Subtracted		188.588	231.109	42.521
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	Divided	1	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Squared			46785.7	58383.2	1.24789
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]			0	3680.39	3222.57	1.14207
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Measured	Subtracted	1	1631.67	2664.55	1032.88
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	Ranked		0	9431	8815	616
	neurocalcin delta. [swissprot;acc:p29554]	Rooted			12.8769	11.6055	1.2714
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared		1	28895.6	35572.8	6677.2
	paxillin. [swissprot;acc:p49023]	Rooted			59.4073	66.7002	7.2929
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Measured		0	2071.59	2133.83	62.24
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Ranked		1	200.691	179.88	20.811
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		Divided		243.583	267.528	1.0983
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]		Subtracted	0	13801.7	13185.9	615.8
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Squared			188.452	230.941	42.489
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	Divided	1	20446.1	24136.4	1.18049
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Ranked		0	11149.7	10571.4	1.0547
	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	Squared	Subtracted	1	28895.6	35572.8	6677.2
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		Divided	0	3680.31	3222.51	1.14206
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Measured	Subtracted	1	1631.67	2664.55	1032.88
	lamin b2. [swissprot;acc:q03252]		Divided	0	579.262	538.704	1.07529
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Rooted		1	77.58	70.0181	1.108
	metastasis-associated protein mta1. [swissprot;acc:q13330]		Subtracted		52.7557	60.035	7.2793
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]		Divided	0	9.92736	9.42407	1.0534
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Ranked	Subtracted	1	200.691	179.88	20.811
	scribble. [refseq;acc:nm_015356]	Rooted		0	18.8966	17.6385	1.2581
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Measured			60	0	60

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.