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 Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1601 to 1650 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
description
Rank
Network Comparison Type
Filtered
red
green
network_comparison
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1757 Divided 1 180.537 178.325 1.0124
1887 Subtracted 2.212
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1862 Divided 210.856 213.147 1.01087
1866 Subtracted 2.291
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1861 Divided 1.01087
1865 Subtracted 2.291
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1511 Divided 213.268 209.509 1.01794
1521 Subtracted 3.759
cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] 2791 Divided 0.00001 0.00001 1
Subtracted 0 0 0
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] 3009 Divided 0.00001 0.00001 1
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] 2402 Divided 182.4 183.083 1.00374
2451 Subtracted 0.683
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 2403 Divided 1.00374
2452 Subtracted 0.683
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 1292 228.644 223.736 4.908
1369 Divided 1.02194
cytochrome c. [swissprot;acc:p00001] 1484 Subtracted 228.419 232.376 3.957
1533 Divided 1.01732
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 420 Subtracted 238.704 255.68 16.976
501 Divided 1.07112
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 1295 Subtracted 220.681 215.78 4.901
1332 Divided 1.02271
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 0.00001 0.00001 1
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 0.00001 1
Subtracted 0 0 0
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 1196 219.354 224.7 5.346
1258 Divided 1.02437
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] 1248 Subtracted 218.368 213.22 5.148
1280 Divided 1.02414
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 1256 Subtracted 5.148
1288 Divided 1.02414
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 124 Subtracted 0 12328.5 10501 1827.5
137 Divided 1.17403
1254 Subtracted 1 218.368 213.22 5.148
1286 Divided 1.02414
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 123 Subtracted 0 12335.3 10506.8 1828.5
136 Divided 1.17403
1252 Subtracted 1 218.368 213.22 5.148
1284 Divided 1.02414
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 126 Subtracted 0 12314.9 10489.3 1825.6
135 Divided 1.17404
1253 Subtracted 1 218.368 213.22 5.148
1285 Divided 1.02414
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 1249 Subtracted 5.148
1281 Divided 1.02414
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 125 Subtracted 0 12314.9 10489.3 1825.6
134 Divided 1.17404

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/