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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Gene Rank Value Type Network Comparison Type description red Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 501 to 550 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
network_comparison
green
251 Divided oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 186.172 1.11707 166.661
Subtracted 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 23.71 267.21
252 Divided eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 1.11689 212.457
Subtracted mad protein (max dimerizer). [swissprot;acc:q05195] 228 23.667 204.333
253 Divided 1.11583
Subtracted nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 251.679 23.642 228.037
254 Divided source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 1.11569 179.88
Subtracted max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 23.642 204.357
255 Divided oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 1.11569 179.88
Subtracted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 23.633 204.366
256 Divided max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1.11569 204.357
Subtracted max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 23.629 204.37
257 Divided 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 1.11569 179.88
Subtracted ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 242.14 23.557 265.697
258 Divided max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 1.11564 204.366
Subtracted gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 23.557 265.697
259 Divided max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 1.11562 204.37
Subtracted adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 23.556 265.696
260 Divided c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 1.11394 196.978
Subtracted surfeit locus protein 5. [swissprot;acc:q15528] 242.14 23.556 265.696
261 Divided heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 1.11394 196.978
Subtracted zinc finger protein 291. [swissprot;acc:q9by12] 242.14 23.556 265.696
262 Divided heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 1.11394 196.978
Subtracted peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 242.14 23.556 265.696
263 Divided heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 1.11394 196.978
Subtracted protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 242.14 23.556 265.696
264 Divided mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 1.11394 196.978
Subtracted 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 23.556 266.796
265 Divided splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 1.11241 202.459
Subtracted 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 23.555 263.798
266 Divided transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 241.07 1.11121 267.88
Subtracted ribosomal protein l10-like protein. [refseq;acc:nm_080746] 243.12 23.542 266.662
267 Divided density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 241.07 1.11121 267.88
Subtracted 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 23.541 266.661
268 Divided eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 1.10996 244.167
Subtracted protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 23.511 265.136
269 Divided cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 241.373 1.10763 267.352
Subtracted 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 23.511 265.136
270 Divided fad synthetase. [refseq;acc:nm_025207] 241.373 1.10763 267.352
Subtracted 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 23.507 265.119
271 Divided 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] 241.373 1.10763 267.352
Subtracted protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 243.072 23.487 266.559
272 Divided ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 1.10763 267.352
Subtracted mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 242.83 23.418 266.248
273 Divided 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] 241.373 1.10763 267.352
Subtracted dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 243.208 23.409 266.617
274 Divided nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 1.10763 267.352
Subtracted 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 23.326 266.07
275 Divided cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 241.373 1.10763 267.352
Subtracted 40s ribosomal protein s5. [swissprot;acc:p46782] 242.473 23.283 265.756

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/