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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Filtered	Gene	Rank	Value Type	description	Network Comparison Type	green	network_comparison	Interaction Map	red

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Showing element 51 to 100 of 3730 in total

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

Rank	description	green	network_comparison	red
51	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	5102	1.40494	7168
52	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	4554.5	1.38688	3284
53	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	syntaxin 10 (syn10). [swissprot;acc:o60499]	19014.6	1.36949	13884.4
55	sedlin. [swissprot;acc:o14582]	16388	1.36929	22440
56	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
57	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	11134.8	1.36581	8152.55
58	dead-box protein. [refseq;acc:nm_018665]	14486	1.36296	10628.3
59	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	11662.3	1.36025	15863.6
60	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	15924	1.35397	11761
61	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	11346.5	1.35302	15352
62	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	12695.6	1.34791	9418.7
63	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	11453	1.34428	8519.83
64	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	20387	1.33563	15264
65	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	10406.3	1.32502	7853.67
66	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	15180	1.32449	11461
67	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	14291.5	1.32408	10793.5
68	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	11823.3	1.32362	8932.56
69	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	10174.1	1.32051	7704.7
70	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	10593.2	1.31931	13975.7
71	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	5700.79	1.31395	4338.65
72	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	5397	1.31027	4119
73	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]	8759.5	1.29915	6742.5
75	nanos (fragment). [sptrembl;acc:q8wy41]	11350	1.29242	8782
76	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	2695	1.28905	3474
77	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	11366.5	1.28853	8821.32
78	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	9706.12	1.27969	7584.72
79	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	12106.5	1.27901	9465.55
80	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	11617.9	1.27636	9102.34
81	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	11356	1.2736	14463
82	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	6058	1.27212	7706.5
83	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	14447.8	1.27077	18359.8
84	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	15781	1.26647	12460.6
85	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	12104.2	1.24934	9688.47
86	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	4546.87	1.24876	5677.96
87	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	4547.43	1.24859	5677.89
88	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	4547.66	1.24852	5677.86
89	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	4549.85	1.24786	5677.58
90	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	4550.87	1.24755	5677.45
91	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	11127.5	1.24387	13841.2
92	dok-like protein. [refseq;acc:nm_024872]	21783	1.23971	17571
93	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	9580.95	1.23793	7739.47
94	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	10519.7	1.23067	12946.3
95	pp3111 protein. [refseq;acc:nm_022156]	7603	1.22926	6185
96	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	10228.3	1.22703	8335.82
97	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
98	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	8858.94	1.22452	7234.6
99	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	10454.7	1.22316	12787.8
100	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	11217.7	1.22151	9183.49

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.