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 4830 to 4879 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2415 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Divided 6956.62 7223.09 1.0383
2416 40s ribosomal protein s23. [swissprot;acc:p39028] Subtracted 3560.63 3381.34 179.29
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Divided 8048.38 7752.09 1.03822
2417 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Subtracted 3560.63 3381.34 179.29
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Divided 3598.55 3467.65 1.03775
2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 4857.03 5039.78 1.03763
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] Subtracted 6294.37 6472.9 178.53
2419 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 3641.4 3462.96 178.44
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 4857.03 5039.78 1.03763
2420 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 3641.45 3463.02 178.43
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 4857.03 5039.78 1.03763
2421 60s ribosomal protein l23a. [swissprot;acc:p29316] Subtracted 3642.13 3463.88 178.25
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Divided 7355.46 7088.93 1.0376
2422 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Subtracted 8285.65 8107.49 178.16
2423 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 3569.06 3392.22 176.84
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 7355.46 7088.93 1.0376
2424 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Subtracted 4418.21 4594.87 176.66
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 7355.46 7088.93 1.0376
2425 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Subtracted 6562.71 6738.23 175.52
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 7355.46 7088.93 1.0376
2426 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Subtracted 6562.71 6738.23 175.52
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided 6123.47 6351.84 1.03729
2427 dynactin 4. [refseq;acc:nm_032486] Subtracted 4644.04 4470.47 173.57
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided 5333.6 5531.41 1.03709
2428 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 4164.76 4337.01 172.25
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Divided 7243.19 7509.81 1.03681
2429 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 3976.92 3804.85 172.07
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

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/