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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1963 to 2012 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
982 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Divided 6654.42 7296.51 1.09649
unr protein. [swissprot;acc:o75534] Subtracted 5195.48 5741.63 546.15
983 tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] 5350.87 5896.82 545.95
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Divided 6654.42 7296.51 1.09649
984 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Subtracted 5568.96 6113.35 544.39
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Divided 6362.64 6976.1 1.09642
985 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Subtracted 3720.18 4264.46 544.28
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Divided 6362.64 6976.1 1.09642
986 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Subtracted 6436.19 6980.13 543.94
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Divided 6362.64 6976.1 1.09642
987 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 6660.04 7301.81 1.09636
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Subtracted 5511.2 6054.71 543.51
988 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] 6618.74 7161.67 542.93
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Divided 6229.69 6829.58 1.0963
989 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted 5707.73 6249.1 541.37
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Divided 11743.3 10712.3 1.09624
990 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 5147.9 5641.25 1.09584
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Subtracted 5707.73 6249.1 541.37
991 single-minded homolog 1. [swissprot;acc:p81133]
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Divided 6472.38 7092.65 1.09583
992 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Subtracted 3119.98 2579.49 540.49
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Divided 5393.37 5909.47 1.09569
993 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 6499.89 7121.77 1.09568
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Subtracted 3119.98 2579.49 540.49
994 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Divided 5800.95 6355.71 1.09563
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 3119.98 2579.49 540.49
995 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Divided 5778.65 6328.56 1.09516
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Subtracted 3119.98 2579.49 540.49
996 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Divided 5110.6 5596.73 1.09512
transcription factor lbx1. [swissprot;acc:p52954] Subtracted 3119.98 2579.49 540.49
997 mosaic protein lgn. [swissprot;acc:p81274]
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Divided 5144.74 5634 1.0951
998 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 3119.98 2579.49 540.49
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Divided 5144.74 5634 1.0951
999 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted 3119.98 2579.49 540.49
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Divided 5680.76 6220.45 1.095
1000 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Subtracted 3119.98 2579.49 540.49
1001 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Divided 5680.76 6220.45 1.095
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Subtracted 10178.5 9638.08 540.42
1002 seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Divided 5680.76 6220.45 1.095
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Subtracted 539.69
1003 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Divided 1.095
1004 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Subtracted 539.69
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Divided 5391.64 5903.72 1.09498
1005 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 5780.34 6329.3 1.09497
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Subtracted 5680.76 6220.45 539.69
1006 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided 5707.73 6249.1 1.09485
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Subtracted 5680.76 6220.45 539.69

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/