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 1691 to 1740 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
846 methyltransferase like 2. [refseq;acc:nm_018396] Divided 147.211 153.371 1.04184
parafibromin. [refseq;acc:nm_024529] Subtracted 239.704 230.991 8.713
847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Divided 147.211 153.371 1.04184
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Subtracted 227.604 219.001 8.603
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Divided 147.211 153.371 1.04184
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 206.214 197.614 8.6
849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Divided 147.211 153.371 1.04184
transcription factor iib. [refseq;acc:nm_013242] Subtracted 206.068 197.471 8.597
850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Divided 107.842 112.329 1.04161
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted 206.068 197.471 8.597
851 n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 8.593
trs85 homolog. [swissprot;acc:q9y2l5] Divided 107.842 112.329 1.04161
852 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted 227.596 219.017 8.579
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Divided 193.114 185.412 1.04154
853 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted 227.596 219.017 8.579
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
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 227.596 219.017 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 178.514 171.42 1.04138
856 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 227.585 219.037 8.548
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Divided 215.028 206.623 1.04068
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

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/