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

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Showing element 1727 to 1776 of 3228 in total

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

Rank	description	red	network_comparison	green
1727	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7]	6260.43	1.06783	6685.05
1728	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	5475.44	1.06782	5127.66
1729	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	6259.8		6684.31
1730	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]		1.06781	6684.3
1731	lamin b2. [swissprot;acc:q03252]	5840.77	1.06776	6236.53
1732	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	5781.8	1.06768	6173.1
1733	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	5874.83	1.06765	6272.26
1734	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]
1735	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
1736	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830]	5925.65	1.06763	6326.43
1737	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]
1738	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	5885.08	1.06761	6282.97
1739	argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	5695.57	1.06743	6079.61
1740	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350]	5878.2	1.06738	6274.27
1741	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	6297.05	1.06734	6721.08
1742	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	6298.76	1.06729	6722.61
1743	histidine-rich membrane protein ke4. [swissprot;acc:q92504]	6298.81		6722.65
1744	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
1745	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	6298.77		6722.62
1746	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	5683.17	1.06728	6065.55
1747	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	9596.59	1.06724	10241.9
1748	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	6301.03	1.06723	6724.63
1749	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	7919.76	1.06721	8452.01
1750	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	5384.89	1.06715	5746.51
1751	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]	6011.57	1.06711	6414.98
1752	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656]	5941.29	1.0671	6339.93
1753	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	5423.67	1.06707	5787.46
1754	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670]	5941.83		6340.32
1755	chromodomain y-like protein 2. [refseq;acc:nm_152342]	7101.7	1.06703	7577.75
1756	40s ribosomal protein s29. [swissprot;acc:p30054]	3582.57	1.067	3357.6
1757	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	7101.15	1.06699	7576.84
1758	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
1759	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	7101.16		7576.87
1760	thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472]	5693.88	1.06698	6075.25
1761	electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	7794.41	1.06692	8316.04
1762	tumor susceptibility gene 101 protein. [swissprot;acc:q99816]	6122.76	1.06672	6531.3
1763	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	5829.73	1.06668	6218.45
1764	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	5829.61	1.06667	6218.27
1765	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]
1766	nitrilase 1. [refseq;acc:nm_005600]
1767	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
1768	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]
1769	dystrophin. [swissprot;acc:p11532]
1770	angiomotin. [refseq;acc:nm_133265]
1771	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
1772	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
1773	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	5829.51	1.06666	6218.11
1774	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	5386.37	1.06656	5744.89
1775	zinc finger protein 258. [refseq;acc:nm_145310]
1776	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]

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.