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 Filtered description Interaction Map Network Comparison Type red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3730 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Filtered
description
red
green
network_comparison
251 0 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 10551.6 11573.6 1.09686
1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 186.172 166.661 1.11707
252 0 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 10551.6 11573.5 1.09685
1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
253 0 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 10551.6 11573.5 1.09685
1 mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 1.11583
254 0 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 10551.6 11573.5 1.09685
1 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 1.11569
255 0 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 10551.6 11573.5 1.09685
1 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 179.88 1.11569
256 0 espin. [refseq;acc:nm_031475] 10551.6 11573.4 1.09684
1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357 1.11569
257 0 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 10552.2 11566.4 1.09611
1 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 1.11569
258 0 40s ribosomal protein s28. [swissprot;acc:p25112] 12967.1 14193.6 1.09459
1 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 204.366 1.11564
259 0 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 10438.3 9549.77 1.09304
1 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 204.37 1.11562
260 0 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 12447.6 11392.6 1.0926
1 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 196.978 1.11394
261 0 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 12448.9 11393.9 1.09259
1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 196.978 1.11394
262 0 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 3464 3778 1.09065
1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 196.978 1.11394
263 0 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 13573.3 14801.2 1.09046
1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 196.978 1.11394
264 0 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 10037.1 10935.1 1.08947
1 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 196.978 1.11394
265 0 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 13653.8 14874 1.08937
1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 202.459 1.11241
266 0 transcription factor btf3 homolog 3. [swissprot;acc:q13892] 13483.3 14685.4 1.08915
1 transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 241.07 267.88 1.11121
267 0 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 8054.34 8772.02 1.0891
1 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 241.07 267.88 1.11121
268 0 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 14257.4 13134.5 1.08549
1 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 244.167 1.10996
269 0 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 12463.5 11482.6 1.08542
1 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 241.373 267.352 1.10763
270 0 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 10735.1 9891.37 1.0853
1 fad synthetase. [refseq;acc:nm_025207] 241.373 267.352 1.10763
271 0 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 10735.1 9891.37 1.0853
1 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] 241.373 267.352 1.10763
272 0 sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 7163.55 7759.61 1.08321
1 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 267.352 1.10763
273 0 wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 12748.1 11770.9 1.08302
1 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] 241.373 267.352 1.10763
274 0 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 10432.4 11298.4 1.08301
1 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 267.352 1.10763
275 0 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 10783 11674.1 1.08264
1 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 241.373 267.352 1.10763

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/