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 2608 to 2657 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
326 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted Subtracted 56.0466 63.4808 7.4342
327 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 21.785
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Rooted Divided 50.3803 45.4193 1.10923
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 243.817 267.962 1.09903
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared 16424.1 20645.8 1.25704
max protein. [swissprot;acc:p25912] Rooted Subtracted 56.3054 63.7148 7.4094
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 6778.4
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured 11773 10733.2 1039.8
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 16067.4 19094.4 1.18839
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 258.437 235.183 1.09888
brain protein 44. [swissprot;acc:o95563] Measured 15999.1 19007.1 1.18801
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared 16442.8 20662.7 1.25664
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 19321 12542.6 6778.4
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted Divided 50.3803 45.4193 1.10923
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked Subtracted 240.801 262.34 21.539
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Rooted 124.41 117.043 7.367
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 11773 10733.2 1039.8
329 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted Divided 50.3803 45.4193 1.10923
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured Subtracted 11773 10733.2 1039.8
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 191.644 170.192 21.452
metaxin 2. [swissprot;acc:o75431] Squared Divided 41236 51807 1.25635
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 19321 12542.6 6778.4
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked Divided 312 284 1.09859
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 15999.1 19007.1 1.18801
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Rooted Subtracted 124.41 117.043 7.367
330 60s ribosomal protein l32. [swissprot;acc:p02433] Divided 50.519 45.5497 1.1091
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked 312 284 1.09859
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 224.657 203.235 21.422
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Measured 11773 10733.2 1039.8
huntingtin interacting protein c. [refseq;acc:nm_012272] Squared Divided 16203.4 20339.9 1.25529
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 19321 12542.6 6778.4
septin 6. [swissprot;acc:q14141] Measured Divided 15959.9 18957.1 1.1878
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted Subtracted 55.5965 62.9349 7.3384
331 apical-like protein (apxl protein). [swissprot;acc:q13796] Divided 60.6697 67.2802 1.10896
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked 312 284 1.09859
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured Subtracted 10246.1 11285.8 1039.7
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 19321 12542.6 6778.4
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 62.9349 7.3384
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Measured Divided 20287.2 17083.8 1.18751
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared 33100.3 41520.6 1.25439
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Subtracted 224.647 203.242 21.405
332 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 12542.6 6778.4
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] Ranked 224.633 203.251 21.382
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 59.0951 66.4332 7.3381
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked Divided 312 284 1.09859
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared 14464.3 18142.8 1.25432
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured 5051.16 5975.51 1.183
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 60.6732 67.2827 1.10894
vav-2 protein. [swissprot;acc:p52735] Measured Subtracted 6660.02 7697.78 1037.76
333 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Rooted 95.4476 102.785 7.3374

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/