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	Gene	Value Type	description	Rank	Filtered	Interaction Map	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1501 to 1550 of 3228 in total

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

description	Rank	red	green	network_comparison
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	1475	181.882	178.438	1.0193
kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]	2198	193.787	195.064	1.00659
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	881	227.604	219.001	1.03928
lactamase, beta 2. [refseq;acc:nm_016027]	2914	0.00001	0.00001	1
lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]	2409	194.407	193.706	1.00362
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	214	191.644	170.192	1.12605
lamin a/c (70 kda lamin). [swissprot;acc:p02545]	2038	218.92	220.811	1.00864
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]	1902	191.411	193.39	1.01034
lamin b1. [swissprot;acc:p20700]	2036	218.919	220.813	1.00865
lamin b2. [swissprot;acc:q03252]	2723	219.323	219.413	1.00041
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	471	248.152	267.226	1.07686
lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697]	1869	220.107	217.75	1.01082
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

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.