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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Gene description Rank Value Type Network Comparison Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 1601 to 1650 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
description
Rank
Network Comparison Type
Filtered
red
network_comparison
green
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 260 Subtracted 1 12515.4 1294.3 11221.1
744 Divided 1.11535
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 784 Subtracted 6289.72 622.24 6911.96
916 Divided 1.09893
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 783 Subtracted 622.24
915 Divided 1.09893
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 928 5638.46 1.09853 6194.04
945 Subtracted 555.58
cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] 2791 Divided 0.00001 1 0.00001
Subtracted 0 0 0
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] 3009 Divided 0.00001 1 0.00001
Subtracted 0 0 0
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 329 11773 1039.8 10733.2
963 Divided 1.09688
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 330 Subtracted 1039.8
964 Divided 1.09688
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 644 4810.85 1.12542 5414.22
825 Subtracted 603.37
cytochrome c. [swissprot;acc:p00001] 2201 Divided 5076.73 1.04916 5326.29
2276 Subtracted 249.56
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 2685 Divided 3953.53 1.00475 3972.32
2720 Subtracted 18.79
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 1299 Divided 5589.33 1.08204 6047.9
1365 Subtracted 458.57
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 3211 Divided 0.00001 1 0.00001
Subtracted 0 0 0
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 2977 Divided 0.00001 1 0.00001
Subtracted 0 0 0
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 1797 6076.66 386.46 6463.12
1877 Divided 1.0636
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 1286 5655.85 1.08218 6120.64
1348 Subtracted 464.79
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 1295 Divided 1.08218
1356 Subtracted 464.79
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 147 Divided 0 292.152 1.29455 378.206
307 Subtracted 86.054
1292 Divided 1 5655.85 1.08218 6120.64
1354 Subtracted 464.79
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 146 Divided 0 291.639 1.29466 377.574
308 Subtracted 85.935
1290 Divided 1 5655.85 1.08218 6120.64
1352 Subtracted 464.79
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 149 Divided 0 293.178 1.29435 379.474
306 Subtracted 86.296
1291 Divided 1 5655.85 1.08218 6120.64
1353 Subtracted 464.79
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 1287 Divided 1.08218
1349 Subtracted 464.79
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 148 Divided 0 293.178 1.29435 379.474
305 Subtracted 86.296

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/