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 9636 to 9685 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
2409 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided Low confidence 7951.8 8195.69 1.03067
2410 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] High confidence 5078.5 5275.76 1.03884
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Subtracted 4857.03 5039.78 182.75
transcription factor bteb1 (basic transcription element binding protein 1) (bte-binding protein 1) (gc box binding protein 1) (krueppel-like factor 9). [swissprot;acc:q13886] Low confidence 7866.49 8109.55 243.06
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Divided 7973.55 8218.08 1.03067
2411 krueppel-like factor 13 (transcription factor bteb3) (basic transcription element binding protein 3) (bte-binding protein 3) (rantes factor of late activated t lymphocytes-1) (rflat-1) (transcription factor nslp1) (novel sp1-like zinc finger transcription factor 1). [swissprot;acc:q9y2y9] Subtracted 7866.84 8109.88 243.04
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Divided High confidence 5078.5 5275.76 1.03884
proto-oncogene tyrosine-protein kinase ros precursor (ec 2.7.1.112) (c-ros-1). [swissprot;acc:p08922] Low confidence 7951.8 8195.68 1.03067
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Subtracted High confidence 4857.03 5039.78 182.75
2412 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 3936.2 3755.33 180.87
dynactin 4. [refseq;acc:nm_032486] Divided 4644.04 4470.47 1.03883
fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] Low confidence 7769.04 8007.2 1.03066
transcription factor sp2. [swissprot;acc:q02086] Subtracted 7866.98 8110.01 243.03
2413 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] Divided High confidence 6956.32 7223.14 1.03836
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 3936.33 3755.5 180.83
transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1] Low confidence 7866.91 8109.94 243.03
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Divided 8199.48 8450.84 1.03066
2414 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] High confidence 6956.32 7223.14 1.03836
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Subtracted 3641.62 3461.4 180.22
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Divided Low confidence 8003.05 8248.37 1.03065
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Subtracted 8073.06 8316.06 243
2415 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 3639.65 3459.64 180.01
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Divided 6956.62 7223.09 1.0383
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Low confidence 7799.23 8038.17 1.03064
pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844] Subtracted 7627.15 7870.14 242.99
2416 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 3560.63 3381.34 179.29
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Divided 8048.38 7752.09 1.03822
fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] Low confidence 7767.54 8005.53 1.03064
transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594] Subtracted 7627.15 7870.14 242.99
2417 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] High confidence 3560.63 3381.34 179.29
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Divided 3598.55 3467.65 1.03775
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Low confidence 7969.73 8213.85 1.03063
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Subtracted 8043.27 8286.26 242.99
2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Divided High confidence 4857.03 5039.78 1.03763
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Subtracted Low confidence 7834.38 8077.35 242.97
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] High confidence 6294.37 6472.9 178.53
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Divided Low confidence 7953.21 8196.83 1.03063
2419 bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] 7969.73 8213.85
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Subtracted 8061.52 8304.37 242.85
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] High confidence 3641.4 3462.96 178.44
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 4857.03 5039.78 1.03763
2420 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 3641.45 3463.02 178.43
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Low confidence 8043.44 8286.28 242.84
phosphorylase b kinase alpha regulatory chain, liver isoform (phosphorylase kinase alpha l subunit). [swissprot;acc:p46019] Divided 7684.95 7920.31 1.03063
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] High confidence 4857.03 5039.78 1.03763
2421 60s ribosomal protein l23a. [swissprot;acc:p29316] Subtracted 3642.13 3463.88 178.25
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Divided 7355.46 7088.93 1.0376
fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] Low confidence 7765.81 8003.6 1.03062
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Subtracted 8368.54 8611.33 242.79
2422 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided High confidence 7355.46 7088.93 1.0376

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/