Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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
Results: HTML CSV LaTeX Showing element 4858 to 4907 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2429 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Divided 7243.19 7509.81 1.03681
2430 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 4164.96 4336.92 171.96
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Divided 7243.07 7509.58 1.0368
2431 60s ribosomal protein l12. [swissprot;acc:p30050] Subtracted 3586.32 3414.42 171.9
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Divided 7242.75 7508.98 1.03676
2432 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 3586.3 3414.4 171.9
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Divided 8154.48 8453.84 1.03671
2433 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 3586.31 3414.41 171.9
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Divided 4585.86 4753.26 1.0365
2434 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted 4368.44 4539.34 170.9
wd repeat domain 26. [refseq;acc:nm_025160] Divided 6423.46 6655.9 1.03619
2435 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 3750.99 3580.35 170.64
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Divided 3669.33 3797.78 1.03501
2436 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 3708.67 3584.47 1.03465
40s ribosomal protein s20. [swissprot;acc:p17075] Subtracted 3590.56 3422.6 167.96
2437 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Divided 3708.67 3584.47 1.03465
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Subtracted 4585.86 4753.26 167.4
2438 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 5637.59 5804.47 166.88
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Divided 7139.06 7384.85 1.03443
2439 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 3754.39 3629.51 1.03441
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Subtracted 5637.59 5804.47 166.88
2440 40s ribosomal protein s3. [swissprot;acc:p23396] 3674.29 3508.13 166.16
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided 4730.66 4891.26 1.03395
2441 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 6477.82 6695.58 1.03362
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Subtracted 3650.78 3484.91 165.87
2442 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Divided 5454.62 5637.88 1.0336
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Subtracted 3650.78 3484.91 165.87
2443 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Divided 3634.59 3756.67 1.03359
surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 3650.8 3484.94 165.86
2444 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Divided 6478.14 6695.67 1.03358
zinc finger protein 291. [swissprot;acc:q9by12] Subtracted 3650.8 3484.94 165.86
2445 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Divided 3633.14 3754.96 1.03353
2446 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 4031.94 4166.99 1.0335
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 3650.8 3484.94 165.86
2447 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided 3730.53 3611.05 1.03309
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Subtracted 3650.82 3484.97 165.85
2448 40s ribosomal protein s16. [swissprot;acc:p17008] Divided 3730.53 3611.05 1.03309
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 3670.45 3504.91 165.54
2449 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 3730.74 3611.45 1.03303
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] Subtracted 7121.07 7286.61 165.54
2450 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 3670.45 3504.91
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Divided 6737.15 6957.34 1.03268
2451 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Subtracted 6469.44 6634.31 164.87
2452 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 3614.08 3450.07 164.01
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Divided 6042.36 6237.19 1.03224
2453 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] 6931.15 7152.73 1.03197
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 3614.07 3450.07 164
2454 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Divided 8751.01 8480.03 1.03196

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.
- http://analysis.yellowcouch.org/