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 25 to 74 of 502 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0

Rank	Hugo	description	red	green	network_comparison
25	no value	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	13730.5	8257	1.66289
26	DTNBP1	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	12128.3	7533.33	1.60995
27	no value	ptd016 protein. [refseq;acc:nm_016125]	18050	11234	1.60673
28	ING5	p28 ing5. [refseq;acc:nm_032329]	12124.8	7562.05	1.60337
29	PNMT	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	7395	11625	1.57201
30	no value	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
31	LRRFIP1	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	8082.33	5266.67	1.53462
32	no value	importin 9. [refseq;acc:nm_018085]	13292.2	8691.76	1.52929
33		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
34	MAPRE2	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	11284	17173.8	1.52196
35	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	3208.8	4871.6	1.5182
36	GNB1L	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	22422	14964	1.4984
37	no value	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	3859	2582	1.49458
38	CDK8	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	7230	10771	1.48976
39	no value	ero1-like. [refseq;acc:nm_014584]	13853	20536	1.48242
40		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	3845	5699	1.48218
41		60s ribosomal protein l21. [swissprot;acc:p46778]	9994.33	6758.83	1.47871
42	SLC25A6	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	8158	5530.5	1.47509
43	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	12143.8	8356.02	1.4533
44	SERPINB12	serpin b12. [swissprot;acc:q96p63]	14604.2	21138.6	1.44743
45	no value	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	14592	21113.7	1.44694
46		60s ribosomal protein l37a. [swissprot;acc:p12751]	12941.7	18499.2	1.42943
47	CYP27B1	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]
48	NDUFA5	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	9830	6909	1.42278
49	no value	brain protein 16. [refseq;acc:nm_016458]	6890.54	4854.99	1.41927
50	COMP	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	9249.73	13091.4	1.41533
51	KPNA2	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	7168	5102	1.40494
52	ARIH2	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	3284	4554.5	1.38688
53	no value	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]
54	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	13884.4	19014.6	1.36949
55	ZNF547	sedlin. [swissprot;acc:o14582]	22440	16388	1.36929
56	no value	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
57	CDC37	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	8152.55	11134.8	1.36581
58	DDX43	dead-box protein. [refseq;acc:nm_018665]	10628.3	14486	1.36296
59	GLUD2	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	15863.6	11662.3	1.36025
60	GNPDA1	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	11761	15924	1.35397
61	CRISP2	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	15352	11346.5	1.35302
62	GLRA3	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	9418.7	12695.6	1.34791
63	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	8519.83	11453	1.34428
64	LYZL1	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	15264	20387	1.33563
65	EP400	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	7853.67	10406.3	1.32502
66	HS6ST2	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	11461	15180	1.32449
67	no value	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	10793.5	14291.5	1.32408
68		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	8932.56	11823.3	1.32362
69		collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	7704.7	10174.1	1.32051
70		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	13975.7	10593.2	1.31931
71	NUP43	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	4338.65	5700.79	1.31395
72	PGAM4	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	4119	5397	1.31027
73	no value	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
74		ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	6742.5	8759.5	1.29915

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.