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 green Gene Network Comparison Type network_comparison Rank Interaction Map red description
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 77072 in total
Filtered  : 0
Value Type  : Measured
green
Network Comparison Type
network_comparison
Rank
Interaction Map
red
description
1068.02 Divided 1.03554 605 Low confidence 1105.98 myoglobin. [swissprot;acc:p02144]
Subtracted 37.96 645
1070.03 Divided 1.07338 339 High confidence 996.883 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]
Subtracted 73.147 320
1079.01 Divided 1.13574 241 1225.47 keratin associated protein 9.2. [refseq;acc:nm_031961]
Subtracted 146.46 218
1079.36 Divided 1.13502 243 1225.09 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
244 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
245 keratin associated protein 1.5. [refseq;acc:nm_031957]
246 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
247 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
Subtracted 145.73 221 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
222 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
223 keratin associated protein 1.5. [refseq;acc:nm_031957]
224 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
225 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
1079.37 Divided 1.135 248 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
249 1225.08 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
250 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
Subtracted 145.71 227 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
228 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
145.72 226 1225.09 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
1079.38 Divided 1.13498 251 1225.08 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
252 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
253 1225.07 espin. [refseq;acc:nm_031475]
Subtracted 145.69 231
145.7 229 1225.08 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
230 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
1079.77 Divided 1.13418 256 1224.65 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]
Subtracted 144.88 234
1081.5 Divided 1.21683 177 Low confidence 1316 small edrk-rich factor 1a. [swissprot;acc:o75920]
Subtracted 234.5 244
1083.48 Divided 1.02198 676 1107.29 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
Subtracted 23.81 721
1084.24 Divided 1.05021 563 1032.4 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]
Subtracted 51.84 595
1084.89 Divided 1.02165 680 1108.38 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]
Subtracted 23.49 724
1086.73 Divided 1.06522 482 1020.19 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]
Subtracted 66.54 535
1087.6 Divided 1.05215 554 1144.32 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
Subtracted 56.72 563
1094.3 Divided 1.03209 622 1129.42 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]
Subtracted 35.12 656
1096.71 Divided 1.08668 429 1191.77 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
430 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
Subtracted 95.06 445 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
446 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
1099.49 Divided 1.1204 366 981.333 jm5 protein. [refseq;acc:nm_007075]
Subtracted 118.157 401

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/