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 5208 to 5257 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2604	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	Divided	214.486	214.184	1.00141
2605	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	Subtracted	224.891	225.195	0.304
	tcd37 homolog; prune. [refseq;acc:nm_021222]	Divided	214.495	214.193	1.00141
2606	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Subtracted	224.891	225.195	0.304
	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	Divided	214.5	214.198	1.00141
2607	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]		215.497	215.799	1.0014
	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	Subtracted	224.891	225.195	0.304
2608	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	Divided	215.497	215.799	1.0014
2609	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]	Subtracted	224.891	225.195	0.304
	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	Divided	215.497	215.799	1.0014
2610	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]
	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]	Subtracted	224.891	225.195	0.304
2611	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]	Divided	215.497	215.799	1.0014
2612	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Subtracted			0.302
	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]	Divided			1.0014
2613	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	Subtracted			0.302
2614	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]		214.502	214.2
	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	Divided	202.821	202.54	1.00139
2615	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	Subtracted	215.497	215.799	0.302
	transcription factor relb (i-rel). [swissprot;acc:q01201]	Divided	202.821	202.54	1.00139
2616	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	Subtracted	214.494	214.192	0.302
	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	Divided	202.821	202.54	1.00139
2617	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]	Subtracted	215.497	215.799	0.302
2618	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]		214.486	214.184
	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	Divided	190.166	190.429	1.00138
2619	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]		220.024	219.722	1.00137
	tcd37 homolog; prune. [refseq;acc:nm_021222]	Subtracted	214.495	214.193	0.302
2620	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	Divided	215.615	215.91	1.00137
	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]	Subtracted	220.024	219.722	0.302
2621	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Divided	224.891	225.195	1.00135
	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]	Subtracted	215.497	215.799	0.302
2622	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]
	zinc finger protein 258. [refseq;acc:nm_145310]	Divided	224.891	225.195	1.00135
2623	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]	Subtracted	215.497	215.799	0.302
	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	Divided	224.891	225.195	1.00135
2624	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	Subtracted	214.5	214.198	0.302
	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	Divided	224.891	225.195	1.00135
2625	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	Subtracted	211.662	211.361	0.301
	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	Divided	204.304	204.028	1.00135
2626	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]		224.891	225.195
	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Subtracted	192.625	192.922	0.297
2627	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]		215.615	215.91	0.295
	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	Divided	224.891	225.195	1.00135
2628	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	Subtracted	202.142	202.436	0.294
2629	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Divided	224.891	225.195	1.00135

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.