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

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/