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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Gene Rank description Value Type Interaction Map red Network Comparison Type Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
Network Comparison Type
green
network_comparison
226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 Divided 269.238 1.12187
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 Subtracted 266.673 24.52
227 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 24.478
thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 Divided 269.234 1.12186
228 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] 244.126 Subtracted 268.604 24.478
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 Divided 202.088 1.12036
229 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 Subtracted 266.663 24.468
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 Divided 202.094 1.12028
230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 Subtracted 267.017 24.323
231 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 Divided 267.881 1.11927
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 Subtracted 202.088 24.323
232 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 24.307
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 239.336 Divided 267.879 1.11926
233 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 Subtracted 259.984 24.257
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 239.32 Divided 267.842 1.11918
234 40s ribosomal protein s23. [swissprot;acc:p39028] 243.944 Subtracted 268.195 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 Divided 256.835 1.11905
235 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 243.944 Subtracted 268.195 24.251
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 227.357 Divided 254.15 1.11785
236 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 Subtracted 228.42 24.224
pp3111 protein. [refseq;acc:nm_022156] 227.357 Divided 254.15 1.11785
237 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 Subtracted 266.18 24.169
syntaxin 18. [swissprot;acc:q9p2w9] 227.357 Divided 254.15 1.11785
238 metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 Subtracted 228.356 24.156
rd protein. [swissprot;acc:p18615] 227.357 Divided 254.15 1.11785
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 Subtracted 267.962 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 Divided 254.15 1.11785
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
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] 252.39 Subtracted 228.297 24.093
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 Divided 254.15 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 Subtracted 265.96 24.068
242 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 265.959 24.067
j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 Divided 254.15 1.11785
243 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 Subtracted 265.945 24.061
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 Divided 254.15 1.11785
244 60s ribosomal protein l5. [swissprot;acc:p46777] 241.899 Subtracted 265.924 24.025
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 Divided 254.15 1.11785
245 60s ribosomal protein l19. [swissprot;acc:p14118] 240.73 Subtracted 264.729 23.999
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 Divided 202.333 1.11751
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 Subtracted 267.528 23.945
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 Divided 212.363 1.11748
247 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 Subtracted 267.527 23.944
rna-binding protein. [refseq;acc:nm_019027] 237.302 Divided 212.41 1.11719
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] 243.583 Subtracted 267.527 23.944
249 ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 Divided 212.41 1.11719
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 Subtracted 202.333 23.776
250 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 Divided 212.41 1.11719
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 Subtracted 186.95 23.743

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/