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

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Showing element 1530 to 1579 of 3228 in total

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

description	Rank	green	network_comparison	red
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960]	2391	215.799	1.00388	214.966
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	1628	214.2	1.01515	217.446
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	272	267.352	1.10763	241.373
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	1	0.00001
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	231	267.881	1.11927	239.336
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	2250	165.058	1.00606	164.064
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	1283	213.22	1.02414	218.368
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]	1260	224.7	1.02437	219.354
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	1897	197.835	1.01035	199.883
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	217.801	1.00727	216.23
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	233	267.842	1.11918	239.32
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	2609	215.799	1.0014	215.497
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	217.175	1.00955	219.25
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4]	1899	197.837	1.01035	199.884
lim/homeobox protein lhx4. [swissprot;acc:q969g2]	1898	197.833		199.881
limb region 1 protein; limb region 1. [refseq;acc:nm_022458]	2469	235.088	1.00308	235.812
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	1482	220.15	1.0191	224.354
limkain b1. [refseq;acc:nm_019081]	703	209.118	1.05413	220.438
limkain beta 2. [refseq;acc:nm_025140]	2096	216.089	1.00756	217.723
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	1987	222.9	1.00952	225.022
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	222.948	1.00929	225.02
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	2027	223.041	1.00885	225.015
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	213.75	1.00154	213.422
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	1738	209.258	1.01289	206.595
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	2465	235.088	1.00308	235.812
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	1347	209.517	1.02223	204.961
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	753	235.583	1.04968	224.434
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	1569	224.767	1.01646	221.128
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	164	249.187	1.19058	209.299
loh1cr12. [refseq;acc:nm_058169]	827	220.579	1.0431	230.087
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	1810	225.827	1.01171	223.214
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	419	253.197	1.08417	233.539
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	205	200.968	1.13501	228.1
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	206	201.006	1.13472	228.085
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	536	227.136	1.06778	242.531
lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980]	3107	0.00001	1	0.00001
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	603	212.945	1.0605	225.829
lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]	2410	193.706	1.00362	194.407
lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]	2412
lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	2116	213.14	1.007	214.632
lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]	2210	200.413	1.00645	199.129
lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]	2929	0.00001	1	0.00001
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	1101	226.584	1.02857	220.291
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	1343	252.916	1.02231	258.558
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	1642	256.531	1.01457	260.269
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	1504	254.797	1.01822	259.439
mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]	2786	0.00001	1	0.00001
mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]	2783

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.