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 1062 to 1111 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
1062 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 269.963 278.239 1.03066
1063 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 1.03064
1064 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 269.955 278.221 1.03062
1065 zinc finger protein 305. [swissprot;acc:o43309] 269.954 278.219
1066 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] 269.956 278.223
1067 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]
1068 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] 269.953 278.215 1.03061
1069 zinc finger protein 232. [swissprot;acc:q9uny5] 269.954 278.218
1070 zinc finger protein 99. [refseq;acc:nm_032164]
1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
1072 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] 269.954 278.217
1073 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] 216.901 210.485 1.03048
1074 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 174.387 179.697 1.03045
1075 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
1076 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
1077 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
1078 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
1079 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
1080 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] 269.896 278.093 1.03037
1081 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 216.875 1.03027
1082 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 220.118 213.685 1.03011
1083 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]
1084 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]
1085 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 231.007 237.864 1.02968
1086 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 236.679 243.679 1.02958
1087 zinc finger protein 277. [swissprot;acc:q9nrm2]
1088 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 219.673 213.378 1.0295
1089 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 121.428 125.004 1.02945
1090 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 226.218 232.88
1091 block 23. [sptrembl;acc:q8nhw5] 226.205 232.858 1.02941
1092 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 226.203 232.855
1093 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 177.432 182.647 1.02939
1094 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 219.655 213.385 1.02938
1095 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 213.552 207.463 1.02935
1096 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 212.345 206.339 1.02911
1097 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 209.123 203.208
1098 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 217.323 211.185 1.02906
1099 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 217.315 211.183 1.02904
1100 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 209.052 203.183 1.02889
1101 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] 220.291 226.584 1.02857
1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 235.974 1.02847
1103 ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 229.441 235.972 1.02846
1104 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 231.922 238.486 1.0283
1105 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 185.882 1.02828
1106 pxr2b protein. [refseq;acc:nm_016559] 212.945 207.109 1.02818
1107 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] 204.603 210.324 1.02796
1108 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 1.02775
1109 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098 212.209
1110 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 1.02769
1111 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 212.123 1.02766

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/