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 7486 to 7535 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1872 proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Squared 29362.2 32156.5 1.09517
quaking isoform 6. [sptrembl;acc:q9p0x9] Rooted 62.1789 64.0173 1.02957
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Measured 6076.66 6463.12 1.0636
1873 40s ribosomal protein s11. [swissprot;acc:p04643] 3618.46 3402.09
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Squared 30483.6 33382.6 1.0951
scratch; scratch 1. [refseq;acc:nm_031309] Ranked 210.55 208.305 1.01078
transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] Rooted 70.1291 72.202 1.02956
1874 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 72.2019
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Measured 6076.66 6463.12 1.0636
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Squared 41376.4 37784 1.09508
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Ranked 223.862 226.271 1.01076
1875 frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] Rooted 70.1291 72.202 1.02956
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Measured 6076.66 6463.14 1.0636
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Squared 14483.5 15859.6 1.09501
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] Ranked 223.862 226.271 1.01076
1876 espin. [refseq;acc:nm_031475] Measured 6076.66 6463.12 1.0636
transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] Rooted 70.1291 72.202 1.02956
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Squared 28394.8 31092.1 1.09499
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Ranked 223.862 226.271 1.01076
1877 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Rooted 63.6973 65.5763 1.0295
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Measured 6076.66 6463.12 1.0636
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Squared 28024.6 30683.7 1.09488
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Ranked 212.186 214.467 1.01075
1878 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Squared 12933 14159.6 1.09484
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Ranked 212.186 214.467 1.01075
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Rooted 52.5662 51.0599 1.0295
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Measured 6076.66 6463.12 1.0636
1879 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Rooted 84.5408 82.1199 1.02948
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Measured 6076.66 6463.12 1.0636
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Ranked 212.186 214.467 1.01075
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Squared 12933 14159.6 1.09484
1880 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Rooted 84.5408 82.1199 1.02948
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Ranked 220.852 223.225 1.01074
d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Measured 6076.66 6463.12 1.0636
serpin b12. [swissprot;acc:q96p63] Squared 26276.4 28767.6 1.09481
1881 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Rooted 84.5408 82.1199 1.02948
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Ranked 210.592 208.355 1.01074
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Measured 6076.68 6462.56 1.0635
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Squared 26276.4 28767.6 1.09481
1882 60s ribosomal protein l28. [swissprot;acc:p46779] Ranked 215.896 213.61 1.0107
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Rooted 84.5408 82.1199 1.02948
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Measured 5490.24 5838.67 1.06346
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Squared 26276.4 28767.6 1.09481
1883 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Measured 5826 6195.48 1.06342
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Ranked 240.317 242.881 1.01067
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Squared 26276.4 28767.6 1.09481
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Rooted 84.5408 82.1199 1.02948
1884 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Measured 5826 6195.48 1.06342
coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Rooted 84.5408 82.1199 1.02948
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Ranked 215.081 217.373 1.01066

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/