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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1708 to 1757 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
854 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Subtracted 219.017 227.596 8.579
855 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018 8.578
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 171.42 178.514 1.04138
856 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 219.037 227.585 8.548
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Divided 206.623 215.028 1.04068
857 midasin (midas-containing protein). [swissprot;acc:q9nu22] Subtracted 228.698 237.218 8.52
putatative 28 kda protein. [refseq;acc:nm_020143] Divided 236.467 227.241 1.0406
858 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted 212.806 221.306 8.5
syntaxin 12. [refseq;acc:nm_177424] Divided 208.997 217.446 1.04043
859 60s ribosomal protein l39. [swissprot;acc:p02404] 224.958 234.025 1.04031
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 42.3003 50.7983 8.498
860 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 224.958 234.025 1.04031
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Subtracted 233.544 242.024 8.48
861 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 224.958 234.025 1.04031
syntaxin 12. [refseq;acc:nm_177424] Subtracted 208.997 217.446 8.449
862 60s ribosomal protein l31. [swissprot;acc:p12947] Divided 224.958 234.025 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 239.778 231.357 8.421
863 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Divided 230.957 240.194 1.03999
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Subtracted 206.623 215.028 8.405
864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Divided 230.957 240.194 1.03999
exocyst complex component sec8. [swissprot;acc:q96a65] Subtracted 209.449 217.762 8.313
865 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 203.814 211.961 1.03997
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Subtracted 278.239 269.963 8.276
866 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 212.806 221.306 1.03994
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Subtracted 278.232 269.96 8.272
867 40s ribosomal protein s3a. [swissprot;acc:p49241] Divided 234.674 225.689 1.03981
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Subtracted 278.223 269.956 8.267
868 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Divided 242.571 233.298 1.03975
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Subtracted 278.223 269.956 8.267
869 exocyst complex component sec8. [swissprot;acc:q96a65] Divided 209.449 217.762 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 278.221 269.955 8.266
870 transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided 203.832 211.908 1.03962
zinc finger protein 305. [swissprot;acc:o43309] Subtracted 278.219 269.954 8.265
871 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 114.552 110.2 1.03949
zinc finger protein 232. [swissprot;acc:q9uny5] Subtracted 278.218 269.954 8.264
872 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Divided 233.272 224.413 1.03948
zinc finger protein 99. [refseq;acc:nm_032164] Subtracted 278.218 269.954 8.264
873 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Divided 233.272 224.413 1.03948
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Subtracted 278.217 269.954 8.263
874 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Divided 203.954 212.002 1.03946
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Subtracted 278.215 269.953 8.262
875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 203.954 212.002 1.03946
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 215.653 223.906 8.253
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Divided 203.954 212.002 1.03946
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 215.653 223.906 8.253
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 203.954 212.002 1.03946
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 278.093 269.896 8.197
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Divided 203.954 212.002 1.03946
syntaxin 7. [swissprot;acc:o15400] Subtracted 209.012 217.181 8.169
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 203.954 212.002 1.03946

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/