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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2132 to 2181 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1066 ZNF18 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Divided 269.956 278.223 1.03062
1067 GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Subtracted 213.552 207.463 6.089
ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 269.956 278.223 1.03062
1068 NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Subtracted 212.345 206.339 6.006
ZNF274 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Divided 269.953 278.215 1.03061
1069 DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Subtracted 229.243 235.246 6.003
ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] Divided 269.954 278.218 1.03061
1070 GIT2 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Subtracted 216.78 222.782 6.002
ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Divided 269.954 278.218 1.03061
1071 no value dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
MPHOSPH10 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Subtracted 241.496 235.508 5.988
1072 PPA1 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 224.307 230.242 5.935
ZNF213 zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Divided 269.954 278.217 1.03061
1073 PPA2 inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Subtracted 224.307 230.242 5.935
WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Divided 216.901 210.485 1.03048
1074 AIPL1 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Subtracted 224.307 230.242 5.935
COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Divided 174.387 179.697 1.03045
1075 AIP ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Subtracted 224.307 230.242 5.935
COPG coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Divided 174.387 179.697 1.03045
1076 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 209.123 203.208 5.915
COPZ1 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Divided 174.387 179.697 1.03045
1077 ARCN1 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 218.098 212.209 5.889
1078 FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 5.887
PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Divided 174.387 179.697 1.03045
1079 COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
SIX1 homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Subtracted 221.286 215.399 5.887
1080 PA2G4 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 221.285 215.4 5.885
ZNF444 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Divided 269.896 278.093 1.03037
1081 FAU 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 216.875 1.03027
SIX2 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Subtracted 221.285 215.401 5.884
1082 ATP2C1 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 5.869
PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Divided 220.118 213.685 1.03011
1083 no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted 217.99 212.123 5.867
SRD5A1 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] Divided 220.118 213.685 1.03011
1084 ATP6V0A1 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Subtracted 218.529 212.676 5.853
SRD5A2 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] Divided 220.118 213.685 1.03011
1085 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Subtracted 218.528 212.676 5.852
DKC1 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Divided 231.007 237.864 1.02968
1086 no value similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 236.679 243.679 1.02958
ATP6V0A4 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Subtracted 218.528 212.676 5.852
1087 no value zinc finger protein 277. [swissprot;acc:q9nrm2] Divided 236.679 243.679 1.02958
TCIRG1 vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Subtracted 218.527 212.676 5.851
1088 ANXA11 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Divided 219.673 213.378 1.0295
PEX5L pxr2b protein. [refseq;acc:nm_016559] Subtracted 212.945 207.109 5.836
1089 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 218.487 212.656 5.831
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Divided 121.428 125.004 1.02945
1090 no value similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 226.218 232.88
NCALD neurocalcin delta. [swissprot;acc:p29554] Subtracted 225.104 230.931 5.827
1091 no value block 23. [sptrembl;acc:q8nhw5] Divided 226.205 232.858 1.02941

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/