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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Filtered Value Type Gene description green Rank network_comparison Interaction Map Network Comparison Type red
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
description
green
Rank
network_comparison
Interaction Map
red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 851.77 131 1.31954 Low confidence 645.504
934.348 37 2.79409 High confidence 334.401
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 4869.42 778 1.00902 Low confidence 4825.89
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 26.1599 19 11.6763 High confidence 305.45
181.734 171 1.22585 Low confidence 222.779
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 1609.88 771 1.01017 1593.68
2642.79 451 1.01545 High confidence 2683.61
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2263.85 474 1.00763 2281.12
2331.31 785 1.00797 Low confidence 2349.9
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 5046.33 492 1.00159 High confidence 5038.33
822 Low confidence
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1932.95 581 1.04278 2015.65
2853.65 438 1.0252 High confidence 2925.57
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 1500.63 459 1.07746 Low confidence 1616.87
1721.76 346 1.06708 High confidence 1837.26
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] 14.3333 121 1.3721 19.6667
3822.12 815 1.00257 Low confidence 3831.93
40s ribosomal protein s10. [swissprot;acc:p46783] 1135.73 513 1.05788 1201.47
40s ribosomal protein s12. [swissprot;acc:p25398] 2194.28 661 1.025 2140.77
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1327.26 346 1.13666 1167.68
1337.54 258 1.13048 High confidence 1183.16
40s ribosomal protein s17. [swissprot;acc:p08708] 146.011 755 1.01203 Low confidence 147.767
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 1735.23 222 1.15728 High confidence 1499.4
2370.67 414 1.09478 Low confidence 2165.44
40s ribosomal protein s25. [swissprot;acc:p25111] 1530.84 736 1.01365 1551.74
40s ribosomal protein s26. [swissprot;acc:p02383] 81.2233 58 1.85588 High confidence 150.741
2484.72 627 1.03073 Low confidence 2410.65
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1650.32 609 1.03491 1594.65
2378.99 444 1.02223 High confidence 2431.87
40s ribosomal protein s28. [swissprot;acc:p25112] 405.367 385 1.04615 387.486
936.963 550 1.05276 Low confidence 890.008
40s ribosomal protein s29. [swissprot;acc:p30054] 1895.38 297 1.10737 High confidence 1711.6
2217.3 356 1.12795 Low confidence 1965.77
40s ribosomal protein s3a. [swissprot;acc:p49241] 2069.56 439 1.08345 1910.16
2879.55 447 1.01735 High confidence 2929.51
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1495.22 255 1.1346 1317.84
1653.68 416 1.09339 Low confidence 1512.43
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 1495.66 254 1.13461 High confidence 1318.22
1651.01 415 1.09373 Low confidence 1509.52
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 838.364 743 1.01302 827.585
1104.61 315 1.09796 High confidence 1212.82
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 142.417 57 1.89769 270.264
67 Low confidence
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 651.607 375 1.11641 583.664
808.929 287 1.11385 High confidence 726.245
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 4231.81 469 1.07113 Low confidence 3950.79
6739.34 313 1.09921 High confidence 6131.07
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 1224.42 380 1.11589 Low confidence 1097.26
1367.83 269 1.12309 High confidence 1217.92
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 1674.32 460 1.07636 Low confidence 1555.54

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/