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 2130 to 2179 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1065 zinc finger protein 305. [swissprot;acc:o43309] Divided 269.954 278.219 1.03062
1066 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 124.434 118.318 6.116
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Divided 269.956 278.223 1.03062
1067 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Subtracted 213.552 207.463 6.089
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 269.956 278.223 1.03062
1068 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
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 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Subtracted 229.243 235.246 6.003
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 269.954 278.218 1.03061
1070 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Subtracted 216.78 222.782 6.002
zinc finger protein 99. [refseq;acc:nm_032164] Divided 269.954 278.218 1.03061
1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Subtracted 241.496 235.508 5.988
1072 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 224.307 230.242 5.935
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Divided 269.954 278.217 1.03061
1073 inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Subtracted 224.307 230.242 5.935
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Divided 216.901 210.485 1.03048
1074 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Subtracted 224.307 230.242 5.935
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Divided 174.387 179.697 1.03045
1075 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Subtracted 224.307 230.242 5.935
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Divided 174.387 179.697 1.03045
1076 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 209.123 203.208 5.915
1077 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Divided 174.387 179.697 1.03045
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 218.098 212.209 5.889
1078 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 5.887
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 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Subtracted 221.286 215.399 5.887
1080 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 221.285 215.4 5.885
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Divided 269.896 278.093 1.03037
1081 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 216.875 1.03027
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Subtracted 221.285 215.401 5.884
1082 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
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Divided 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]
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted 217.99 212.123 5.867
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] Divided 220.118 213.685 1.03011
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
1085 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Divided 231.007 237.864 1.02968
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
1086 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]
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Divided 236.679 243.679 1.02958
1087 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
zinc finger protein 277. [swissprot;acc:q9nrm2] Divided 236.679 243.679 1.02958
1088 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 219.673 213.378 1.0295
pxr2b protein. [refseq;acc:nm_016559] Subtracted 212.945 207.109 5.836
1089 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 218.487 212.656 5.831
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 neurocalcin delta. [swissprot;acc:p29554] Subtracted 225.104 230.931 5.827

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/