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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 1701 to 1750 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
851 Divided KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] 1.04161 107.842 112.329
Subtracted MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 8.593 227.601 219.008
852 Divided HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 1.04154 193.114 185.412
Subtracted GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 8.579 227.596 219.017
853 Divided WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 1.0414 108.289 112.772
Subtracted no value 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] 8.579 227.596 219.017
854 Divided CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 1.0414 108.289 112.772
Subtracted NDUFS8 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] 8.579 227.596 219.017
855 Divided CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 1.04138 178.514 171.42
Subtracted ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 8.578 227.596 219.018
856 Divided XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 1.04068 215.028 206.623
Subtracted MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 8.548 227.585 219.037
857 Divided PNO1 putatative 28 kda protein. [refseq;acc:nm_020143] 1.0406 227.241 236.467
Subtracted MDN1 midasin (midas-containing protein). [swissprot;acc:q9nu22] 8.52 237.218 228.698
858 Divided STX12 syntaxin 12. [refseq;acc:nm_177424] 1.04043 217.446 208.997
Subtracted SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 8.5 221.306 212.806
859 Divided no value 60s ribosomal protein l39. [swissprot;acc:p02404] 1.04031 234.025 224.958
Subtracted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 8.498 50.7983 42.3003
860 Divided 60s ribosomal protein l18a. [swissprot;acc:q02543] 1.04031 234.025 224.958
Subtracted NOL6 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 8.48 242.024 233.544
861 Divided RPS19 40s ribosomal protein s19. [swissprot;acc:p39019] 1.04031 234.025 224.958
Subtracted STX12 syntaxin 12. [refseq;acc:nm_177424] 8.449 217.446 208.997
862 Divided RPL31 60s ribosomal protein l31. [swissprot;acc:p12947] 1.04031 234.025 224.958
Subtracted PKM2 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] 8.421 231.357 239.778
863 Divided CSNK2A1P casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 1.03999 240.194 230.957
Subtracted XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 8.405 215.028 206.623
864 Divided CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 1.03999 240.194 230.957
Subtracted EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] 8.313 217.762 209.449
865 Divided BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 1.03997 211.961 203.814
Subtracted ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 8.276 269.963 278.239
866 Divided SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 1.03994 221.306 212.806
Subtracted no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 8.272 269.96 278.232
867 Divided 40s ribosomal protein s3a. [swissprot;acc:p49241] 1.03981 225.689 234.674
Subtracted ZNF18 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 8.267 269.956 278.223
868 Divided MVD diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 1.03975 233.298 242.571
Subtracted ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 8.267 269.956 278.223
869 Divided EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] 1.03969 217.762 209.449
Subtracted ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 8.266 269.955 278.221
870 Divided no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 1.03962 211.908 203.832
Subtracted ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] 8.265 269.954 278.219
871 Divided CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 1.03949 110.2 114.552
Subtracted ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] 8.264 269.954 278.218
872 Divided HNRPK heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 1.03948 224.413 233.272
Subtracted ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] 8.264 269.954 278.218
873 Divided PRPF4 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] 1.03948 224.413 233.272
Subtracted ZNF213 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 8.263 269.954 278.217
874 Divided PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 1.03946 212.002 203.954
Subtracted ZNF274 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 8.262 269.953 278.215
875 Divided PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 1.03946 212.002 203.954
Subtracted JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 8.253 223.906 215.653

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
- Hugo is the HGNC identifier if it exists
- 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/