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 1980 to 2029 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
990 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] High confidence 5147.9 5641.25 1.09584
991 bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] Low confidence 7962.23 8267.24 1.03831
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] High confidence 6472.38 7092.65 1.09583
992 gp25l2 protein. [refseq;acc:nm_017510] Low confidence 8667.6 8999.51 1.03829
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] High confidence 5393.37 5909.47 1.09569
993 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Low confidence 7982.87 8288.57 1.03829
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] High confidence 6499.89 7121.77 1.09568
994 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 5800.95 6355.71 1.09563
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Low confidence 8203.04 8516.96 1.03827
995 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] High confidence 5778.65 6328.56 1.09516
gem-interacting protein. [refseq;acc:nm_016573] Low confidence 8619.95 8949.84 1.03827
996 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] High confidence 5110.6 5596.73 1.09512
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Low confidence 8153.64 8465.6 1.03826
997 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] High confidence 5144.74 5634 1.0951
spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Low confidence 6992.03 7259.31 1.03823
998 reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] 8202.26 8515.65 1.03821
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] High confidence 5144.74 5634 1.0951
999 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] Low confidence 6995.37 7262.5 1.03819
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] High confidence 5680.76 6220.45 1.095
1000 af-4 protein (proto-oncogene af4) (fel protein). [swissprot;acc:p51825] Low confidence 6995.5 7262.62 1.03818
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] High confidence 5680.76 6220.45 1.095
1001 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Low confidence 6995.47 7262.59 1.03818
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] High confidence 5680.76 6220.45 1.095
1002 all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 6995.48 7262.6 1.03818
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] High confidence 5680.76 6220.45 1.095
1003 seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Low confidence 6998.01 7265 1.03815
1004 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] High confidence 5391.64 5903.72 1.09498
sh3 domain-binding protein 5 (sh3 domain-binding protein that preferentially associates with btk). [swissprot;acc:o60239] Low confidence 7804.72 8102.42 1.03814
1005 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] High confidence 5780.34 6329.3 1.09497
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Low confidence 8039.58 8345.65 1.03807
1006 gk001 protein. [refseq;acc:nm_020198] 8422.24 8742.91
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] High confidence 5707.73 6249.1 1.09485
1007 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] Low confidence 8161.56 8472.15 1.03806
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 5707.73 6249.1 1.09485
1008 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 6913.4 7176.31 1.03803
single-minded homolog 1. [swissprot;acc:p81133] High confidence 5707.73 6249.1 1.09485
1009 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439] Low confidence 8086.9 8394.45 1.03803
synapsin iii. [swissprot;acc:o14994] High confidence 5791.82 6340.86 1.0948
1010 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Low confidence 7733.46 8027.45 1.03802
1011 calponin h1, smooth muscle (basic calponin) (calponin 1). [swissprot;acc:p51911] 8087.01 8394.5
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] High confidence 5791.82 6340.86 1.0948
1012 actin binding lim protein 2. [refseq;acc:nm_032432]
calponin, acidic isoform (calponin 3). [swissprot;acc:q15417] Low confidence 8087 8394.49 1.03802
1013 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 7733.95 8028.03
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] High confidence 5791.82 6340.86 1.0948
1014 dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Low confidence 7878.21 8177.69 1.03801
synapsin ii. [swissprot;acc:q92777] High confidence 5791.82 6340.86 1.0948
1015 mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]

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/