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 Value Type description Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 508 to 557 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
254 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided 200.691 1.11569 179.88
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 227.999 23.633 204.366
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 200.691 1.11569 179.88
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 227.999 23.629 204.37
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 1.11569 204.357
257 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 200.691 179.88
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Subtracted 242.14 23.557 265.697
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 227.999 1.11564 204.366
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Subtracted 242.14 23.556 265.696
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 227.999 1.11562 204.37
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 1.11394 196.978
surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 242.14 23.556 265.696
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided 219.421 1.11394 196.978
zinc finger protein 291. [swissprot;acc:q9by12] Subtracted 242.14 23.556 265.696
262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 219.421 1.11394 196.978
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 242.14 23.556 265.696
263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 219.421 1.11394 196.978
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 242.14 23.556 265.696
264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 219.421 1.11394 196.978
265 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 240.243 23.555 263.798
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 225.217 1.11241 202.459
266 ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 243.12 23.542 266.662
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 241.07 1.11121 267.88
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 23.541 266.661
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Divided 241.07 1.11121 267.88
268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 1.10996 244.167
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 241.625 23.511 265.136
269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Divided 241.373 1.10763 267.352
270 40s ribosomal protein s3. [swissprot;acc:p23396] Subtracted 241.612 23.507 265.119
fad synthetase. [refseq;acc:nm_025207] Divided 241.373 1.10763 267.352
271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 243.072 23.487 266.559
272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Divided 241.373 1.10763 267.352
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 23.418 266.248
273 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Divided 241.373 1.10763 267.352
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Subtracted 243.208 23.409 266.617
274 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 23.326 266.07
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Divided 241.373 1.10763 267.352
275 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 242.473 23.283 265.756
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Divided 241.373 1.10763 267.352
276 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 1.10716 266.969
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 258.437 23.254 235.183
277 40s ribosomal protein s29. [swissprot;acc:p30054] Divided 241.849 1.10665 267.642
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 239.277 23.157 262.434
278 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 241.399 1.10642 267.088
myelin gene expression factor 2. [refseq;acc:nm_016132] Subtracted 235.383 23.093 258.476
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 252.644 1.10605 228.42

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/