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 15030 to 15079 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1879 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Ranked Divided 212.186 214.467 1.01075
nucleoporin like 1. [refseq;acc:nm_014089] Measured Subtracted 6174.74 6538.73 363.99
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Squared Divided 12933 14159.6 1.09484
1880 calmegin precursor. [swissprot;acc:o14967] Ranked Subtracted 217.48 215.256 2.224
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Squared 27825.3 30004.3 2179
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Rooted Divided 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
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Rooted Subtracted 61.5765 63.4381 1.8616
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Measured 6174.74 6538.73 363.99
serpin b12. [swissprot;acc:q96p63] Squared Divided 26276.4 28767.6 1.09481
1881 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Ranked Subtracted 217.48 215.256 2.224
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Measured 6174.74 6538.73 363.99
coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Rooted Divided 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
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Subtracted 27825.3 30004.3 2179
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Rooted 62.7784 64.64 1.8616
1882 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
60s ribosomal protein l28. [swissprot;acc:p46779] Ranked Divided 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 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Measured Subtracted 5423.67 5787.46 363.79
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided 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
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Subtracted 27825.3 30004.3 2179
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Ranked 217.48 215.256 2.224
1883 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Rooted 62.901 64.7621 1.8611
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Measured Divided 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
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Ranked Subtracted 217.48 215.256 2.224
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Measured 5949.31 6313.1 363.79
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Squared 24214.1 26392.2 2178.1
1884 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Ranked 221.607 219.386 2.221
adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Measured Divided 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
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Squared Subtracted 24797.6 26975 2177.4
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Measured 5633.44 5997 363.56
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Ranked Divided 215.081 217.373 1.01066
upf0183 protein. [swissprot;acc:q9bsu1] Squared 26276.4 28767.6 1.09481
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Rooted Subtracted 61.1874 63.0474 1.86
1885 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] Squared Divided 26276.4 28767.6 1.09481
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Ranked 204.44 206.615 1.01064
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 180.609 178.393 2.216
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Squared 24803.3 26978.5 2175.2
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Rooted Divided 61.8736 63.6965 1.02946
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Subtracted 60.4307 58.5724 1.8583
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] Measured 5633.44 5997 363.56

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/