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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1713 to 1762 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
857 midasin (midas-containing protein). [swissprot;acc:q9nu22] Subtracted 237.218 228.698 8.52
putatative 28 kda protein. [refseq;acc:nm_020143] Divided 227.241 236.467 1.0406
858 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted 221.306 212.806 8.5
syntaxin 12. [refseq;acc:nm_177424] Divided 217.446 208.997 1.04043
859 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 1.04031
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 50.7983 42.3003 8.498
860 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 234.025 224.958 1.04031
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Subtracted 242.024 233.544 8.48
861 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 234.025 224.958 1.04031
syntaxin 12. [refseq;acc:nm_177424] Subtracted 217.446 208.997 8.449
862 60s ribosomal protein l31. [swissprot;acc:p12947] Divided 234.025 224.958 1.04031
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Subtracted 231.357 239.778 8.421
863 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Divided 240.194 230.957 1.03999
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Subtracted 215.028 206.623 8.405
864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Divided 240.194 230.957 1.03999
exocyst complex component sec8. [swissprot;acc:q96a65] Subtracted 217.762 209.449 8.313
865 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 211.961 203.814 1.03997
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Subtracted 269.963 278.239 8.276
866 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 221.306 212.806 1.03994
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Subtracted 269.96 278.232 8.272
867 40s ribosomal protein s3a. [swissprot;acc:p49241] Divided 225.689 234.674 1.03981
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Subtracted 269.956 278.223 8.267
868 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Divided 233.298 242.571 1.03975
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Subtracted 269.956 278.223 8.267
869 exocyst complex component sec8. [swissprot;acc:q96a65] Divided 217.762 209.449 1.03969
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Subtracted 269.955 278.221 8.266
870 transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided 211.908 203.832 1.03962
zinc finger protein 305. [swissprot;acc:o43309] Subtracted 269.954 278.219 8.265
871 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 110.2 114.552 1.03949
zinc finger protein 232. [swissprot;acc:q9uny5] Subtracted 269.954 278.218 8.264
872 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Divided 224.413 233.272 1.03948
zinc finger protein 99. [refseq;acc:nm_032164] Subtracted 269.954 278.218 8.264
873 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Divided 224.413 233.272 1.03948
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Subtracted 269.954 278.217 8.263
874 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Divided 212.002 203.954 1.03946
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Subtracted 269.953 278.215 8.262
875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 212.002 203.954 1.03946
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 223.906 215.653 8.253
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Divided 212.002 203.954 1.03946
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 223.906 215.653 8.253
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 212.002 203.954 1.03946
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 269.896 278.093 8.197
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Divided 212.002 203.954 1.03946
syntaxin 7. [swissprot;acc:o15400] Subtracted 217.181 209.012 8.169
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 212.002 203.954 1.03946
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Subtracted 217.491 209.323 8.168
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 212.002 203.954 1.03946
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Subtracted 217.491 209.323 8.168
881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 227.604 219.001 1.03928
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 211.961 203.814 8.147

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.
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