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 2430 to 2479 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
608 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared 24560.6 29071.1 1.18365
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Measured 4510.61 5098.74 1.13039
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Rooted 59.6517 64.4642 1.08068
609 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Measured 3886.62 3438.82 1.13022
histone h2b.s (h2b/s). [swissprot;acc:p57053] Ranked 247.47 233.441 1.0601
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted 62.9281 67.99 1.08044
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Squared 12276.9 14526 1.1832
610 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Rooted 136.706 126.565 1.08012
histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked 247.47 233.441 1.0601
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1.12907
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Squared 12347.6 14594.8 1.18199
611 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 23487.1 27726.3 1.18049
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured 5148.71 5811.74 1.12878
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked 247.47 233.441 1.0601
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted 51.0091 55.0909 1.08002
612 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Measured 3975.77 4485.05 1.1281
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Rooted 57.1949 61.7633 1.07987
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Ranked 247.47 233.441 1.0601
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Squared 18595.6 21936.3 1.17965
613 histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked 247.47 233.441 1.0601
n-myc proto-oncogene protein. [swissprot;acc:p04198] Rooted 57.1971 61.7626 1.07982
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Squared 17550.2 20701.1 1.17954
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 3975.77 4485.05 1.1281
614 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Squared 51527.6 43689.1 1.17942
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 1.07973
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Ranked 214.257 202.125 1.06002
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Measured 11222.2 9948.93 1.12798
615 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Squared 51527.6 43689.1 1.17942
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured 11222.2 9948.93 1.12798
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Rooted 57.2007 61.7615 1.07973
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Ranked 214.257 202.132 1.05999
616 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Measured 11222.2 9948.93 1.12798
coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Squared 51527.6 43689.1 1.17942
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Ranked 214.257 202.132 1.05999
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted 57.2007 61.7615 1.07973
617 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared 51527.6 43689.1 1.17942
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Measured 5162.52 5822.47 1.12783
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Rooted 57.2008 61.7614 1.07973
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Ranked 214.257 202.135 1.05997
618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted 57.208 61.7592 1.07956
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured 7878.27 8879.08 1.12703
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 1.17942
619 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
dendritic cell protein. [refseq;acc:nm_006360] Rooted 63.847 68.8873 1.07894
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Ranked 214.256 202.139 1.05994
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Measured 3879.99 4371.24 1.12661
620 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Ranked 214.256 202.14 1.05994
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared 32208.8 37986.6 1.17939

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/