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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3964 to 4013 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
991 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Rooted 52.2349 55.1039 1.05492
992 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Squared 18885.2 21708.3 1.14949
mstp028 protein. [refseq;acc:nm_031954] Rooted 61.7824 65.1711 1.05485
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Measured 5393.37 5909.47 1.09569
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Ranked 218.468 211.357 1.03364
993 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Measured 6499.89 7121.77 1.09568
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Squared 29881.4 34348 1.14948
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Ranked 211.071 204.205 1.03362
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Rooted 61.7884 65.1721 1.05476
994 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Measured 5800.95 6355.71 1.09563
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Ranked 116.845 120.772 1.03361
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Squared 18761.8 21564.5 1.14938
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Rooted 61.7917 65.1727 1.05472
995 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Measured 5778.65 6328.56 1.09516
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Squared 25141.4 28896.8 1.14937
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Ranked 219.656 212.547 1.03345
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Rooted 61.7923 65.1728 1.05471
996 j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 69.5394 73.3277 1.05448
lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Squared 25141.4 28896.8 1.14937
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Measured 5110.6 5596.73 1.09512
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Ranked 219.656 212.547 1.03345
997 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Rooted 69.5394 73.3277 1.05448
lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Squared 25141.4 28896.8 1.14937
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Ranked 219.656 212.547 1.03345
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Measured 5144.74 5634 1.0951
998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Ranked 225.557 218.271 1.03338
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Squared 25141.4 28896.8 1.14937
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Measured 5144.74 5634 1.0951
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Rooted 69.5394 73.3277 1.05448
999 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Squared 25141.4 28896.8 1.14937
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Measured 5680.76 6220.45 1.095
vinculin (metavinculin). [swissprot;acc:p18206] Ranked 215.92 208.95 1.03336
1000 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Measured 5680.76 6220.45 1.095
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Squared 27225.4 31287.9 1.14922
kinesin protein. [refseq;acc:nm_032559] Rooted 59.2757 62.5044 1.05447
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Ranked 225.167 217.922 1.03325
1001 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Rooted 67.7551 71.4422 1.05442
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Squared 21068.2 24205.2 1.1489
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] Measured 5680.76 6220.45 1.095
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Ranked 225.167 217.922 1.03325
1002 40s ribosomal protein s30. [swissprot;acc:q05472] Rooted 61.3513 64.6874 1.05438
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Measured 5680.76 6220.45 1.095
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Squared 21068.2 24205.2 1.1489
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Ranked 225.167 217.922 1.03325
1003 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Squared 17541.4 20148.6 1.14863
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Rooted 59.2915 62.5118 1.05431
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Measured 5680.76 6220.45 1.095
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Ranked 225.167 217.922 1.03325
1004 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Squared 17541.4 20148.6 1.14863

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/