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 1651 to 1700 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
413 rd protein. [swissprot;acc:p18615] Rooted 55.5489 50.535 1.09922
vav proto-oncogene. [swissprot;acc:p15498] Measured 6644.99 7707.8 1.15994
414 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Squared 22109.6 26989.4 1.22071
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted 55.5489 50.535 1.09922
katanin p60 subunit a 1. [refseq;acc:nm_007044] Ranked 232.431 252.238 1.08522
415 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Rooted 55.5489 50.535 1.09922
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Ranked 232.382 252.166 1.08514
vav-3 protein. [swissprot;acc:q9ukw4] Measured 6647.43 7706.18 1.15927
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared 29160.4 35570.2 1.21981
416 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Rooted 55.5489 50.535 1.09922
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Ranked 240.6 261.041 1.08496
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Measured 4509.54 5223.95 1.15842
prohibitin. [swissprot;acc:p35232] Squared 22841.8 27856.2 1.21953
417 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Measured 4522.71 5233.14 1.15708
j domain containing protein 1. [swissprot;acc:q9ukb3] Rooted 55.5489 50.535 1.09922
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Squared 22841.8 27856.2 1.21953
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Ranked 233.539 253.197 1.08417
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Measured 5493.1 6350.19 1.15603
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Ranked 233.539 253.197 1.08417
e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 1.21791
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Rooted 55.5489 50.535 1.09922
419 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Squared 24832.1 30242.8 1.21789
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Rooted 55.5489 50.535 1.09922
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Measured 5493.1 6350.19 1.15603
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 233.539 253.197 1.08417
420 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared 30924.3 37652.3 1.21756
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Ranked 233.539 253.197 1.08417
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Rooted 51.7959 56.9253 1.09903
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured 10235.2 11830.8 1.15589
421 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted 50.4666 45.9317 1.09873
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared 36933 44953.6 1.21717
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Ranked 223.202 205.9 1.08403
vav-2 protein. [swissprot;acc:p52735] Measured 6660.02 7697.78 1.15582
422 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 50.4641 45.9293 1.09873
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Squared 25860 31475.4 1.21715
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured 5206.9 6010.04 1.15425
ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 1.08284
423 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted 50.4663 45.9313 1.09873
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Measured 5207.03 6010.1 1.15423
ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked 240.287 260.193 1.08284
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 1.21652
424 60s ribosomal protein l23a. [swissprot;acc:p29316] Rooted 50.4703 45.9373 1.09868
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 1.08284
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Squared 20259.5 24635.7 1.21601
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Measured 5207.78 6010.45 1.15413
425 40s ribosomal protein s20. [swissprot;acc:p17075] Rooted 50.0161 45.5318 1.09849
max protein. [swissprot;acc:p25912] Ranked 227.828 210.561 1.082
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Squared 20258.6 24634.7 1.21601
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Measured 3729.02 4301.58 1.15354

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/