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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 4477 to 4526 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2239 testis-specific bromodomain protein. [refseq;acc:nm_001726] Divided 222.958 224.336 1.00618
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Subtracted 193.787 195.064 1.277
2240 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
nag14 protein. [refseq;acc:nm_022143] Divided 222.959 224.337 1.00618
2241 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96 224.338
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] Subtracted 202.414 203.691 1.277
2242 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Divided 209.197 207.915 1.00617
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Subtracted 193.787 195.064 1.277
2243 integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Divided 209.197 207.915 1.00617
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Subtracted 195.97 194.7 1.27
2244 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Divided 209.197 207.915 1.00617
sipl protein. [refseq;acc:nm_018269] Subtracted 208.609 207.346 1.263
2245 e-1 enzyme. [refseq;acc:nm_021204] 208.315 207.061 1.254
fibulin-2 precursor. [swissprot;acc:p98095] Divided 191.618 190.448 1.00614
2246 leng5 protein. [refseq;acc:nm_024075] Subtracted 221.599 220.351 1.248
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Divided 223.58 224.943 1.0061
2247 sipl protein. [refseq;acc:nm_018269] 208.609 207.346 1.00609
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Subtracted 221.599 220.351 1.248
2248 kinesin-like protein kif3c. [swissprot;acc:o14782] Divided 219.045 220.377 1.00608
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 221.599 220.351 1.248
2249 pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Divided 181.091 179.999 1.00607
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Subtracted 221.599 220.351 1.248
2250 likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided 164.064 165.058 1.00606
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted 221.599 220.351 1.248
2251 e-1 enzyme. [refseq;acc:nm_021204] Divided 208.315 207.061 1.00606
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Subtracted 212.563 211.315 1.248
2252 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 200.95 199.711 1.239
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Divided 217.185 218.498 1.00605
2253 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 219.047 220.371 1.00604
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 125.845 127.083 1.238
2254 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 125.912 127.146 1.234
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Divided 193.065 194.22 1.00598
2255 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] 202.366 203.57 1.00595
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Subtracted 213.391 214.606 1.215
2256 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 217.419 218.627 1.208
seven in absentia homolog 2. [refseq;acc:nm_005067] Divided 223.546 224.869 1.00592
2257 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] Subtracted 202.366 203.57 1.204
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Divided 212.563 211.315 1.00591
2258 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Subtracted 216.622 215.436 1.186
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Divided 223.888 225.191 1.00582
2259 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 213.391 214.606 1.00569
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Subtracted 216.622 215.436 1.186
2260 leng5 protein. [refseq;acc:nm_024075] Divided 221.599 220.351 1.00566
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Subtracted 211.597 210.416 1.181
2261 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Divided 221.599 220.351 1.00566
2262 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Subtracted 211.597 210.416 1.181
2263 splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] 219.652 218.482 1.17
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Divided 221.599 220.351 1.00566

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/