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 5358 to 5407 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1340 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Squared 18734 21102.7 1.12644
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Ranked 226.433 231.491 1.02234
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Measured 5979.07 6453.53 1.07935
1341 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 5887.82 6354.58 1.07928
alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Rooted 62.4321 65.0012 1.04115
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Ranked 226.433 231.491 1.02234
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Squared 18734 21102.7 1.12644
1342 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Measured 5887.86 6354.51 1.07926
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Ranked 226.433 231.491 1.02234
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Rooted 60.8644 63.3676 1.04113
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Squared 18734 21102.7 1.12644
1343 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 26357.4 29687.5 1.12634
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Measured 5887.86 6354.5 1.07925
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Ranked 258.558 252.916 1.02231
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Rooted 60.8644 63.3676 1.04113
1344 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Measured 5887.86 6354.5 1.07925
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Ranked 216.772 221.594 1.02224
helicase (fragment). [sptrembl;acc:q92771] Squared 26354.7 29683.8 1.12632
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Rooted 61.688 64.2216 1.04107
1345 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Measured 5887.88 6354.47 1.07925
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Rooted 62.7228 65.296 1.04102
phd finger protein 9. [refseq;acc:nm_018062] Ranked 216.772 221.594 1.02224
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Squared 16944.3 19083.4 1.12624
1346 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Rooted 62.7228 65.296 1.04102
alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Measured 5887.89 6354.45 1.07924
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Squared 29909.9 33684.3 1.12619
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Ranked 216.772 221.594 1.02224
1347 aarf domain containing kinase 4. [refseq;acc:nm_024876] Rooted 62.7228 65.296 1.04102
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Squared 14123.5 15905.2 1.12615
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Ranked 204.961 209.517 1.02223
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Measured 6153.36 6640.77 1.07921
1348 aarf domain containing kinase 1. [refseq;acc:nm_020421] Rooted 62.7228 65.296 1.04102
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Measured 6153.36 6640.77 1.07921
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Squared 29911.6 33682.9 1.12608
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Ranked 218.569 213.832 1.02215
1349 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Rooted 62.138 64.6833 1.04096
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Squared 29911.8 33682.7 1.12607
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Measured 6153.36 6640.77 1.07921
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Ranked 218.572 213.841 1.02212
1350 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Squared 29911.7 33682.8 1.12607
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Rooted 62.1427 64.6863 1.04093
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Measured 6783.78 7320.39 1.0791
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Ranked 218.574 213.847 1.0221
1351 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] Measured 6105.23 6587.88 1.07906
prohibitin. [swissprot;acc:p35232] Ranked 211.513 206.941 1.02209
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Squared 14753.6 16612.9 1.12602
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Rooted 61.6779 64.2009 1.04091
1352 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Measured 6104.11 6586.48 1.07902
megf6 (fragment). [sptrembl;acc:o75095] Rooted 61.7068 64.2305 1.0409
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Squared 26925.7 30311.3 1.12574

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/