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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description Filtered Rank Gene Value Type Network Comparison Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Filtered
Rank
red
network_comparison
green
28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 1 2530 3880.5 1.02431 3788.42
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 0.00001 1 0.00001
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 0 492 5038.33 1.00159 5046.33
1 2756 0.00001 1 0.00001
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2302 6946.6 1.04565 7263.68
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714] 3180 0.00001 1 0.00001
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 2105 6916.14 1.05481 7295.24
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 0 438 2925.57 1.0252 2853.65
1 1898 6885.11 1.0628 7317.48
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 0 346 1837.26 1.06708 1721.76
1 2305 6946.82 1.04564 7263.87
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 563 5480.24 1.13536 6222.04
3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] 1274 5885 1.08261 6371.14
3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] 1275
3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 2547 3370.46 1.02187 3444.18
38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2261 6486.84 1.04615 6786.23
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 0 121 19.6667 1.3721 14.3333
1 1469 5473.09 1.07571 5887.45
40s ribosomal protein s11. [swissprot;acc:p04643] 1873 3618.46 1.0636 3402.09
40s ribosomal protein s13. [swissprot;acc:q02546] 1498 5414.98 1.07456 5818.7
40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 2436 3708.67 1.03465 3584.47
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 0 258 1183.16 1.13048 1337.54
1 2067 3602.75 1.05616 3411.18
40s ribosomal protein s15a. [swissprot;acc:p39027] 2008 3637.47 1.05876 3435.61
40s ribosomal protein s16. [swissprot;acc:p17008] 2448 3730.53 1.03309 3611.05
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 2437 3708.67 1.03465 3584.47
40s ribosomal protein s19. [swissprot;acc:p39019] 807 4708.61 1.11003 5226.71
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 0 222 1499.4 1.15728 1735.23
1 2242 3670.45 1.04723 3504.91
40s ribosomal protein s20. [swissprot;acc:p17075] 2211 3590.56 1.04907 3422.6
40s ribosomal protein s21. [swissprot;acc:p35265] 2403 5078.5 1.03884 5275.76
40s ribosomal protein s23. [swissprot;acc:p39028] 2152 3560.63 1.05302 3381.34
40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1599 5184.45 1.07147 5554.97
40s ribosomal protein s26. [swissprot;acc:p02383] 0 58 150.741 1.85588 81.2233
1 1655 5488.7 1.06953 5131.89
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 0 444 2431.87 1.02223 2378.99
1 2126 4806.33 1.05422 5066.92
40s ribosomal protein s28. [swissprot;acc:p25112] 0 385 387.486 1.04615 405.367
1 700 7161.14 1.11936 8015.92
40s ribosomal protein s29. [swissprot;acc:p30054] 0 297 1711.6 1.10737 1895.38
1 1756 3582.57 1.067 3357.6
40s ribosomal protein s3. [swissprot;acc:p23396] 2235 3674.29 1.04736 3508.13
40s ribosomal protein s30. [swissprot;acc:q05472] 1145 5893.97 1.08858 6416.07
40s ribosomal protein s3a. [swissprot;acc:p49241] 0 447 2929.51 1.01735 2879.55
1 2263 4918.64 1.0461 5145.39
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 0 255 1317.84 1.1346 1495.22
1 1974 3678.62 1.05993 3470.64
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 254 1318.22 1.13461 1495.66
1 1967 3678.56 1.05994 3470.55

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/