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

Results: HTML CSV LaTeX

Showing element 5014 to 5063 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	red	green	network_comparison
1254	Ranked	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	219.354	224.7	1.02437
	Squared	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	26773.9	30358.8	1.1339
	Rooted	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	62.4299	65.2404	1.04502
1255	Measured	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	5438.66	5893.87	1.0837
	Ranked	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	219.354	224.7	1.02437
	Squared	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	22337.6	25320.9	1.13356
	Rooted	gtp binding protein 2. [refseq;acc:nm_019096]	62.4299	65.2404	1.04502
1256	Measured	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	10719	9891.08	1.0837
	Ranked	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	219.354	224.699	1.02437
	Squared	transportin-sr; importin 12. [refseq;acc:nm_012470]	22037.5	24968.1	1.13298
	Rooted	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	62.4299	65.2404	1.04502
1257	Measured	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318]	5438.66	5893.87	1.0837
	Ranked	espin. [refseq;acc:nm_031475]	219.354	224.7	1.02437
	Squared	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	22008	24929.4	1.13274
	Rooted	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]	62.4299	65.2404	1.04502
1258	Measured	glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	6251.32	6774.12	1.08363
	Ranked	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]	219.354	224.7	1.02437
	Squared	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	23019.8	26073.1	1.13264
	Rooted	sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]	62.4299	65.2404	1.04502
1259	Measured	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204]	5685.38	6157.7	1.08308
	Ranked	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	219.354	224.7	1.02437
	Squared	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	13834.4	15664	1.13225
	Rooted	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]	62.4299	65.2404	1.04502
1260	Measured	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	5754.84	6232.83	1.08306
	Ranked	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]	219.354	224.7	1.02437
	Squared	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	31586.9	35762.8	1.1322
	Rooted	sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]	62.4299	65.2404	1.04502
1261	Measured	epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929]	5685.34	6157.53	1.08305
	Ranked	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]	219.354	224.7	1.02437
	Squared	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	15483.8	17529.5	1.13212
	Rooted	xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]	62.4299	65.2404	1.04502
1262	Measured	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	5894.47	6383.73	1.083
	Ranked	keratin associated protein 9.2. [refseq;acc:nm_031961]	219.353	224.678	1.02428
	Squared	zinc finger protein 277. [swissprot;acc:q9nrm2]	15483.8	17529.5	1.13212
	Rooted	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	76.053	79.4727	1.04496
1263	Measured	gtp binding protein 2. [refseq;acc:nm_019096]	5894.47	6383.73	1.083
	Ranked	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	171.231	167.177	1.02425
	Squared	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	16151.6	18284.1	1.13203
	Rooted	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	76.024	79.4409	1.04495
1264	Measured	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	5894.47	6383.73	1.083
	Ranked	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	171.231	167.177	1.02425
	Squared	endothelial-derived gene 1. [refseq;acc:nm_025205]	26062.8	29502.8	1.13199
	Rooted	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	67.018	70.0209	1.04481
1265	Measured	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]	5894.47	6383.73	1.083
	Ranked	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	171.231	167.177	1.02425
	Squared	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	13562.4	15352.3	1.13198
	Rooted	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	57.8563	55.3779	1.04475
1266	Measured	sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]	5894.47	6383.73	1.083
	Ranked	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	171.231	167.177	1.02425
	Squared	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	22590.9	25571.8	1.13195

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.