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 7386 to 7435 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1847 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Measured 6215.55 6613.46 1.06402
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Squared 26990.9 29579.6 1.09591
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Rooted 68.9584 71.0209 1.02991
1848 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 64.27 66.1875 1.02984
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Ranked 218.441 216.064 1.011
heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Measured 5746.06 6113.79 1.064
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Squared 30518.9 33445.2 1.09588
1849 apical-like protein (apxl protein). [swissprot;acc:q13796] 30517.3 33442.4 1.09585
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Measured 6267.93 6668.72 1.06394
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Ranked 218.445 216.074 1.01097
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Rooted 61.8519 63.6966 1.02982
1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Ranked 215.931 213.587 1.01097
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Squared 26167 28674.3 1.09582
protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] Measured 6158.6 6551.94 1.06387
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Rooted 65.0281 66.9647 1.02978
1851 adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] Measured 6156.28 6549.03 1.0638
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] Squared 26167.1 28674.2 1.09581
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Ranked 218.448 216.08 1.01096
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 61.8466 63.6861 1.02974
1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Ranked 196.008 198.154 1.01095
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Measured 6271.17 6670.97 1.06375
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Squared 26167.1 28674.2 1.09581
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Rooted 63.7444 65.6383 1.02971
1853 keratin associated protein 9.2. [refseq;acc:nm_031961] Measured 6076.65 6463.64 1.06368
nitrilase 1. [refseq;acc:nm_005600] Squared 26167.1 28674.2 1.09581
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 61.8436 63.6804 1.0297
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Ranked 217.924 215.564 1.01095
1854 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Rooted 62.7784 64.64 1.02965
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Measured 6076.66 6463.14 1.0636
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Ranked 222.215 224.637 1.0109
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Squared 26167.1 28674.2 1.09581
1855 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Rooted 62.7784 64.64 1.02965
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Ranked 217.891 215.542 1.0109
keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Measured 6076.66 6463.14 1.0636
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Squared 26167.1 28674.2 1.09581
1856 dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Rooted 62.7784 64.64 1.02965
dystrophin. [swissprot;acc:p11532] Squared 26167.1 28674.2 1.09581
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Ranked 217.892 215.543 1.0109
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Measured 6076.66 6463.14 1.0636
1857 angiomotin. [refseq;acc:nm_133265] Squared 26167.1 28674.2 1.09581
ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Rooted 62.7784 64.64 1.02965
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Measured 6076.66 6463.15 1.0636
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Ranked 222.215 224.637 1.0109
1858 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] Squared 26167.1 28674.2 1.09581
ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Rooted 62.7784 64.64 1.02965
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Ranked 217.893 215.545 1.01089
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Measured 6076.66 6463.13 1.0636
1859 adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Rooted 62.7784 64.64 1.02965
alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] Squared 26167.1 28674.2 1.09581
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Ranked 217.895 215.547 1.01089

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/