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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Value Type Gene Rank green Network Comparison Type Interaction Map description network_comparison red Filtered
Results: HTML CSV LaTeX Showing element 451 to 500 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
green
Network Comparison Type
description
network_comparison
red
226 266.673 Subtracted protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 24.52 242.153
269.238 Divided cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1.12187 239.991
227 268.604 Subtracted methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 24.478 244.126
269.234 Divided thrombospondin 3 precursor. [swissprot;acc:p49746] 1.12186 239.99
228 202.088 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] 1.12036 226.411
268.604 Subtracted 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] 24.478 244.126
229 202.094 Divided breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1.12028 226.401
266.663 Subtracted 60s ribosomal protein l3-like. [swissprot;acc:q92901] 24.468 242.195
230 267.017 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 24.323 242.694
267.915 Divided cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 1.11934 239.35
231 202.088 Subtracted 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] 24.323 226.411
267.881 Divided likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1.11927 239.336
232 202.094 Subtracted breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 24.307 226.401
267.879 Divided smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1.11926 239.336
233 259.984 Subtracted 60s ribosomal protein l7. [swissprot;acc:p18124] 24.257 235.727
267.842 Divided lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 1.11918 239.32
234 256.835 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 1.11905 287.41
268.195 Subtracted 40s ribosomal protein s23. [swissprot;acc:p39028] 24.251 243.944
235 254.15 Divided phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 1.11785 227.357
268.195 Subtracted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 24.251 243.944
236 228.42 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 24.224 252.644
254.15 Divided pp3111 protein. [refseq;acc:nm_022156] 1.11785 227.357
237 syntaxin 18. [swissprot;acc:q9p2w9]
266.18 Subtracted mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 24.169 242.011
238 228.356 metastasis-associated protein mta1. [swissprot;acc:q13330] 24.156 252.512
254.15 Divided rd protein. [swissprot;acc:p18615] 1.11785 227.357
239 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
267.962 Subtracted dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 24.145 243.817
240 228.297 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] 24.093 252.39
254.15 Divided androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 1.11785 227.357
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
265.96 Subtracted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 24.068 241.892
242 254.15 Divided j domain containing protein 1. [swissprot;acc:q9ukb3] 1.11785 227.357
265.959 Subtracted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 24.067 241.892
243 254.15 Divided sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1.11785 227.357
265.945 Subtracted 60s ribosomal protein l23a. [swissprot;acc:p29316] 24.061 241.884
244 254.15 Divided ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 1.11785 227.357
265.924 Subtracted 60s ribosomal protein l5. [swissprot;acc:p46777] 24.025 241.899
245 202.333 Divided small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 1.11751 226.109
264.729 Subtracted 60s ribosomal protein l19. [swissprot;acc:p14118] 23.999 240.73
246 212.363 Divided eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 1.11748 237.312
267.528 Subtracted 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 23.945 243.583
247 212.41 Divided rna-binding protein. [refseq;acc:nm_019027] 1.11719 237.302
267.527 Subtracted 60s ribosomal protein l12. [swissprot;acc:p30050] 23.944 243.583
248 212.41 Divided apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 1.11719 237.302
267.527 Subtracted dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 23.944 243.583
249 202.333 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 23.776 226.109
212.41 Divided ns1-associated protein 1. [refseq;acc:nm_006372] 1.11719 237.302
250 186.95 Subtracted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 23.743 210.693
212.41 Divided heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 1.11719 237.302

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/