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 Gene Rank Value Type Filtered Interaction Map Network Comparison Type red network_comparison green
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 19268 in total
Value Type  : Measured
description
Rank
Filtered
Interaction Map
Network Comparison Type
red
network_comparison
green
cop9 complex subunit 7a; cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7a. [refseq;acc:nm_016319] 3332 1 Low confidence Divided 7996.92 1.0267 8210.43
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 264 High confidence 4987.58 1.2181 4094.57
448 Subtracted 893.01
3176 Low confidence Divided 7797.64 1.02737 8011.03
3313 Subtracted 213.39
cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] 2114 High confidence 6773.67 301.84 7075.51
2206 Low confidence Divided 7864.03 1.03139 8110.9
2298 Subtracted 246.87
2330 High confidence Divided 6773.67 1.04456 7075.51
cop9 constitutive photomorphogenic homolog subunit 7b; likely ortholog of cop9 (constitutive photomorphogenic), subunit 7b (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7b. [refseq;acc:nm_022730] 3340 Low confidence Subtracted 7997.29 212.86 8210.15
3356 Divided 1.02662
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 146 0 High confidence Subtracted 17356 230 17126
325 Low confidence 8820 152 8668
456 High confidence Divided 17356 1.01343 17126
702 Low confidence 8820 1.01754 8668
2827 1 High confidence 0.00001 1 0.00001
Subtracted 0 0 0
3174 Low confidence Divided 7797.64 1.02737 8011.03
3311 Subtracted 213.39
cop9 signalosome complex subunit 2 (signalosome subunit 2) (sgn2) (thyroid receptor interacting protein 15) (trip15). [swissprot;acc:q15647] 2841 High confidence Divided 0.00001 1 0.00001
Subtracted 0 0 0
3175 Low confidence Divided 7797.64 1.02737 8011.03
3312 Subtracted 213.39
cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] 2108 High confidence 6773.67 301.84 7075.51
2324 Divided 1.04456
2423 Low confidence 7904.53 1.03061 8146.48
2436 Subtracted 241.95
copper chaperone for superoxide dismutase (superoxide dismutase copper chaperone). [swissprot;acc:o14618] 2027 Divided 7780.94 1.03204 8030.23
2217 Subtracted 249.29
copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 610 8631.91 361.25 8993.16
765 Divided 1.04185
1711 High confidence Subtracted 5941.29 398.64 6339.93
1752 Divided 1.0671
copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 584 Low confidence Subtracted 8644.06 366.89 9010.95
736 Divided 1.04244
1712 High confidence Subtracted 5941.83 398.49 6340.32
1754 Divided 1.06707
coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551] 2686 Subtracted 7913.63 26.31 7939.94
2734 Divided 1.00332
3400 Low confidence Subtracted 8072.49 210.54 8283.03
3482 Divided 1.02608
core promoter element-binding protein (kruppel-like factor 6) (b-cell derived protein 1) (proto-oncogene bcd1) (transcription factor zf9) (gc-rich sites binding factor gbf). [swissprot;acc:q99612] 3964 Subtracted 9140.87 180.81 9321.68
4246 Divided 1.01978
core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951] 3183 High confidence 0.00001 1 0.00001
Subtracted 0 0 0
5059 Low confidence Divided 0.00001 1 0.00001
Subtracted 0 0 0
core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] 151 10492.4 687.67 9804.73
214 Divided 1.07014
coronin 1b (coronin 2). [swissprot;acc:q9br76] 2595 Subtracted 7985.56 236.85 8222.41

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/