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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 951 to 1000 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
green
network_comparison
red
238 metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 1 228.356 24.156 252.512
rd protein. [swissprot;acc:p18615] Divided 254.15 1.11785 227.357
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Subtracted 267.962 24.145 243.817
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 254.15 1.11785 227.357
keratin associated protein 1.5. [refseq;acc:nm_031957] Subtracted 0 11573.7 1022.1 10551.6
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 9795.36 1.09969 8907.41
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 1 254.15 1.11785 227.357
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 228.297 24.093 252.39
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 0 11573.7 1022.1 10551.6
methyltransferase like 2. [refseq;acc:nm_018396] Divided 16326 1.09923 17946
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 1 254.15 1.11785 227.357
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Subtracted 265.96 24.068 241.892
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 11573.7 1022.1 10551.6
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Divided 12743.3 1.09891 14003.7
242 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 13895.8 1.09822 15260.6
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 1 265.959 24.067 241.892
j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 254.15 1.11785 227.357
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Subtracted 0 11573.6 1022 10551.6
243 60s ribosomal protein l23a. [swissprot;acc:p29316] 1 265.945 24.061 241.884
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 11573.5 1021.9 10551.6
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Divided 1373 1.09752 1251
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1 254.15 1.11785 227.357
244 60s ribosomal protein l5. [swissprot;acc:p46777] Subtracted 265.924 24.025 241.899
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided 254.15 1.11785 227.357
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Subtracted 0 11573.5 1021.9 10551.6
keratin associated protein 9.2. [refseq;acc:nm_031961] Divided 11579.9 1.09751 10551.1
245 60s ribosomal protein l19. [swissprot;acc:p14118] Subtracted 1 264.729 23.999 240.73
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Divided 0 13019 1.09702 11867.6
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Subtracted 11573.5 1021.9 10551.6
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 1 202.333 1.11751 226.109
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 267.528 23.945 243.583
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Divided 212.363 1.11748 237.312
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 0 11573.7 1.09687 10551.6
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Subtracted 11573.5 1021.9
247 60s ribosomal protein l12. [swissprot;acc:p30050] 1 267.527 23.944 243.583
espin. [refseq;acc:nm_031475] 0 11573.4 1021.8 10551.6
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Divided 11573.7 1.09687
rna-binding protein. [refseq;acc:nm_019027] 1 212.41 1.11719 237.302
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 267.527 23.944 243.583
keratin associated protein 1.5. [refseq;acc:nm_031957] Divided 0 11573.7 1.09687 10551.6
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Subtracted 9878.1 1021.3 10899.4
249 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 11566.4 1014.2 10552.2
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Divided 11573.7 1.09687 10551.6
ns1-associated protein 1. [refseq;acc:nm_006372] 1 212.41 1.11719 237.302
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 202.333 23.776 226.109
250 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided 212.41 1.11719 237.302
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 11573.7 1.09687 10551.6
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Subtracted 1 186.95 23.743 210.693
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 0 13514.5 991.8 12522.7

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/