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 2273 to 2322 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
285 40s ribosomal protein s28. [swissprot;acc:p25112] Rooted 0 13.5612 12.5026 1.08467
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 1 48.4278 54.2262 1.11973
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Measured 0 2698.62 3010.22 1.11547
Ranked 10686 9925.58 1.07661
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 1 23326.5 19296.4 1.20885
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked 224.647 203.242 1.10532
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Squared 0 208.691 170.202 1.22614
286 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Measured 5497.01 6127.24 1.11465
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Ranked 12228.2 11367.3 1.07573
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1 224.633 203.251 1.1052
exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Rooted 0 54.8943 59.4407 1.08282
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 188.588 231.109 1.22547
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted 1 51.8717 46.3287 1.11965
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Squared 6693.64 8564.94 1.27956
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 1.10517
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Measured 0 726.245 808.929 1.11385
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Squared 188.452 230.941 1.22546
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 6693.64 8564.94 1.27956
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 1.11965
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 0 34.7164 32.0874 1.08193
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 1 23303.1 19279.5 1.2087
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked 0 17842.7 16590.3 1.07549
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1 240.758 266.078 1.10517
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 14930.6 16053 1.07517
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 1 23422.4 19380.3 1.20857
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Squared 0 188.176 230.603 1.22546
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 6693.64 8564.94 1.27956
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Measured 0 1293.73 1161.64 1.11371
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 1 51.8789 46.3416 1.11949
my016 protein. [sptrembl;acc:q9h3k6] 0 37.7009 34.862 1.08143
289 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 5868.74 4797.35 1.22333
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Rooted 28.6008 30.8974 1.0803
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Ranked 15147.2 14091.9 1.07489
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1 272.781 246.892 1.10486
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 6693.64 8564.94 1.27956
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 1.11899
tubby protein homolog. [swissprot;acc:p50607] Measured 0 3797.57 4228.27 1.11341
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 1 4682.88 5646.19 1.20571
290 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared 15734.4 20126.8 1.27916
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 75.6323 67.6572 1.11788
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 0 22.6917 24.5013 1.07975
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured 1370.82 1525.56 1.11288
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Squared 6188.69 7568.12 1.2229
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Ranked 15147.2 14091.9 1.07489
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 1 231.969 210.064 1.10428
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 4991.48 6014.08 1.20487
291 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Ranked 0 10922.9 11731.8 1.07406
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] 1 251.679 228.037 1.10368

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/