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 2401 to 2450 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1201 keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Subtracted 219.354 224.699 5.345
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Divided 210.986 216.344 1.0254
1202 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 227.274 233.041 1.02537
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Subtracted 219.354 224.699 5.345
1203 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Divided 219.023 213.606 1.02536
1204 keratin associated protein 1.5. [refseq;acc:nm_031957] Subtracted 219.354 224.699 5.345
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Divided 219.022 213.607 1.02535
1205 keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Subtracted 219.354 224.699 5.345
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Divided 224.805 219.251 1.02533
1206 integral membrane protein cii-3b. [sptrembl;acc:o75609] 207.646 212.891 1.02526
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Subtracted 219.354 224.699 5.345
1207 keratin associated protein 4.4. [refseq;acc:nm_032524]
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Divided 207.644 212.888 1.02525
1208 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Subtracted 219.354 224.699 5.345
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 224.878 219.342 1.02524
1209 succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] 207.931 213.175 1.02522
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Subtracted 146.036 140.692 5.344
1210 keratin associated protein 9.2. [refseq;acc:nm_031961] 219.353 224.678 5.325
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Divided 224.764 219.241 1.02519
1211 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 214.364 219.759 1.02517
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 174.387 179.697 5.31
1212 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Divided 214.364 219.759 1.02517
1213 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Subtracted 174.387 179.697 5.31
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Divided 214.364 219.759 1.02517
1214 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Subtracted 174.387 179.697 5.31
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Divided 214.364 219.759 1.02517
1215 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 218.268 212.916 1.02514
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Subtracted 174.387 179.697 5.31
1216 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Divided 218.269 212.918 1.02513
1217 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 217.258 1.025
hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted 221.093 226.399 5.306
1218 fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Divided 211.959 217.258 1.025
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 221.093 226.399 5.306
1219 coactosin-like protein. [swissprot;acc:q14019] Divided 211.959 217.258 1.025
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Subtracted 221.093 226.399 5.306
1220 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 217.258 5.299
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Divided 1.025
1221 fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Subtracted 5.299
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Divided 1.025
1222 coactosin-like protein. [swissprot;acc:q14019] Subtracted 5.299
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Divided 206.774 211.936 1.02496
1223 tumor protein d52 (n8 protein). [swissprot;acc:p55327] 206.771 211.926 1.02493
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Subtracted 211.959 217.258 5.299
1224 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Divided 225.906 231.524 1.02487
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted 211.959 217.258 5.299
1225 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 219.55 214.288 5.262
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 166.846 170.989 1.02483

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/