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

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Showing element 1513 to 1562 of 3228 in total

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

description	Rank	red	green	network_comparison
langerhans cell specific c-type lectin. [refseq;acc:nm_015717]	3046	0.00001	0.00001	1
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]	1870	220.107	217.75	1.01082
lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	2529	221.776	222.283	1.00229
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379]	2293	200.158	201.213	1.00527
late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	3044	0.00001	0.00001	1
lats homolog 1. [refseq;acc:nm_004690]	2057	218.79	216.981	1.00834
lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	2053
lbp-9. [refseq;acc:nm_014553]	1193	220.742	215.237	1.02558
leng5 protein. [refseq;acc:nm_024075]	2260	221.599	220.351	1.00566
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	2693	188.193	188.049	1.00077
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	3017	0.00001	0.00001	1
leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]	3153
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	470	248.152	267.226	1.07686
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	2677	144.412	144.553	1.00098
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	468	248.152	267.226	1.07686
leucyl-trna synthetase. [refseq;acc:nm_020117]	1735	218.99	216.189	1.01296
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	798	224.244	234.511	1.04578
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960]	2391	214.966	215.799	1.00388
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	1628	217.446	214.2	1.01515
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	272	241.373	267.352	1.10763
likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]	2898	0.00001	0.00001	1
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	231	239.336	267.881	1.11927
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	2250	164.064	165.058	1.00606
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	1283	218.368	213.22	1.02414
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]	1260	219.354	224.7	1.02437
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	1897	199.883	197.835	1.01035
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290]	1896
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]	2107	216.23	217.801	1.00727
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	233	239.32	267.842	1.11918
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	2609	215.497	215.799	1.0014
lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]	2611
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	1983	219.25	217.175	1.00955
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]	1899	199.884	197.837	1.01035
lim/homeobox protein lhx4. [swissprot;acc:q969g2]	1898	199.881	197.833
limb region 1 protein; limb region 1. [refseq;acc:nm_022458]	2469	235.812	235.088	1.00308
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	1482	224.354	220.15	1.0191
limkain b1. [refseq;acc:nm_019081]	703	220.438	209.118	1.05413
limkain beta 2. [refseq;acc:nm_025140]	2096	217.723	216.089	1.00756
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	1987	225.022	222.9	1.00952
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165]	2001	225.02	222.948	1.00929
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	2027	225.015	223.041	1.00885
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]	2582	213.422	213.75	1.00154
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	1738	206.595	209.258	1.01289
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	2465	235.812	235.088	1.00308
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	1347	204.961	209.517	1.02223
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	753	224.434	235.583	1.04968
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	1569	221.128	224.767	1.01646
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	164	209.299	249.187	1.19058
loh1cr12. [refseq;acc:nm_058169]	827	230.087	220.579	1.0431
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	1810	223.214	225.827	1.01171

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.