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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
description Rank Gene Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
Interaction Map
red
green
network_comparison
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 2962 Low confidence 200.017 196.692 1.0169
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 2474 High confidence 216.64 217.285 1.00298
2595 Low confidence 200.484 196.948 1.01795
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 1991 199.582 195.763 1.01951
2327 High confidence 217.413 218.426 1.00466
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] 2321 Low confidence 198.366 194.732 1.01866
2395 High confidence 218.192 219.014 1.00377
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] 1637 202.358 199.408 1.01479
2163 Low confidence 200.982 197.22 1.01908
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] 2478 High confidence 216.177 216.801 1.00289
3515 Low confidence 200.312 197.374 1.01489
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 857 204.36 199.229 1.02575
2368 High confidence 218.555 219.434 1.00402
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 2269 217.419 218.627 1.00556
3038 Low confidence 200.303 197.031 1.01661
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] 2174 197.69 193.995 1.01905
2367 High confidence 217.589 218.475 1.00407
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2316 217.241 218.311 1.00493
3393 Low confidence 198.522 195.526 1.01532
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] 2329 High confidence 217.112 218.116 1.00462
2798 Low confidence 200.64 197.228 1.0173
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 1918 199.382 195.527 1.01972
2175 High confidence 210.209 208.808 1.00671
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 2440 217.645 218.376 1.00336
2613 Low confidence 200.463 196.947 1.01785
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036] 1432 High confidence 220.987 225.468 1.02028
2995 Low confidence 199.67 196.383 1.01674
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 1832 200.092 196.175 1.01997
2432 High confidence 215.807 216.556 1.00347
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] 2355 217.232 218.162 1.00428
3198 Low confidence 200.29 197.129 1.01604
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] 1798 200.037 196.088 1.02014
2525 High confidence 215.835 216.341 1.00234
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 2077 Low confidence 200.371 196.58 1.01928
2620 High confidence 215.615 215.91 1.00137
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] 2150 217.871 219.366 1.00686
2964 Low confidence 200.589 197.26 1.01688
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] 70 259.517 235.017 1.10425
810 High confidence 212.386 221.785 1.04425
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 325 243.944 268.195 1.09941
4510 Low confidence 208.988 210.759 1.00847
28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 729 205.65 200.165 1.0274
2212 High confidence 224.411 225.854 1.00643
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 9 Low confidence 58 44 1.31818
23 High confidence
28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] 1659 217.925 214.826 1.01443
2664 Low confidence 201.194 197.699 1.01768
28s ribosomal protein s18b, mitochondrial precursor (mrp-s18-b) (mrps18b) (mrp-s18-2) (ptd017 protein) (hspc183). [swissprot;acc:q9y676] 3958 201.908 204.37 1.01219
28s ribosomal protein s18c, mitochondrial precursor (mrp-s18-c) (mrps18c) (mrp-s18-1) (cgi-134). [swissprot;acc:q9y3d5] 3329 200.825 197.742 1.01559
28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 730 206.555 201.05 1.02738

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/