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

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/