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 11814 to 11863 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1477 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Rooted Divided 63.207 65.62 1.03818
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Ranked Subtracted 207.013 211.05 4.037
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Divided 215.328 211.267 1.01922
1478 40s ribosomal protein s19. [swissprot;acc:p39019] Squared Subtracted 18854.4 21540.4 2686
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Ranked Divided 215.122 211.066 1.01922
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Measured 5659.22 6084.68 1.07518
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Rooted Subtracted 56.8891 54.5075 2.3816
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Divided 65.7121 68.2158 1.0381
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Measured Subtracted 6176.82 6617.91 441.09
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Ranked 205.817 209.851 4.034
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Squared Divided 26860.7 29969 1.11572
1479 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 18854.4 21540.4 2686
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] Ranked 205.817 209.851 4.034
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Rooted 56.8889 54.5073 2.3816
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Measured Divided 5787.03 6221.72 1.07511
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Rooted 65.7121 68.2158 1.0381
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Ranked 228.469 232.855 1.0192
parafibromin. [refseq;acc:nm_024529] Measured Subtracted 4331.17 4771.22 440.05
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Squared Divided 26860.7 29969 1.11572
1480 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Ranked 218.664 214.55 1.01918
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Measured 5660.17 6085.22 1.07509
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Squared 15124.2 16872.9 1.11562
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Rooted Subtracted 60.6322 63.0093 2.3771
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Divided 65.7121 68.2158 1.0381
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Ranked Subtracted 213.251 209.264 3.987
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Squared 28751.1 31432.6 2681.5
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Measured 5770.74 6210.65 439.91
1481 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] Squared Divided 26142.6 29163.8 1.11557
alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Ranked Subtracted 225.148 221.177 3.971
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 208.432 204.516 1.01915
dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] Measured Subtracted 5692.34 6131.71 439.37
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 3688.8 3431.33 1.07504
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Rooted Subtracted 51.9837 54.3601 2.3764
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Squared 26278.9 28944.8 2665.9
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Rooted Divided 63.582 66.002 1.03806
1482 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Ranked Subtracted 225.148 221.177 3.971
enigma protein; lim domain protein. [refseq;acc:nm_005451] Rooted Divided 61.1844 63.5127 1.03805
leng5 protein. [refseq;acc:nm_024075] Measured 5372.25 5775.21 1.07501
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Ranked 224.354 220.15 1.0191
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Rooted Subtracted 60.4911 58.1154 2.3757
protein bap28. [swissprot;acc:q9h583] Squared Divided 14997.9 16728.4 1.11538
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Subtracted 26625.9 29291.6 2665.7
ubiquitin. [swissprot;acc:p02248] Measured 6158.22 6597.55 439.33
1483 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Squared Divided 31810.3 35473.9 1.11517
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Rooted 61.1844 63.5127 1.03805
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Subtracted 60.4911 58.1154 2.3757
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Ranked Divided 198.927 202.726 1.0191
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Subtracted 228.419 232.376 3.957
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Measured Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 6048.57 6487.65 439.08

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/