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

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/