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 19170 to 19219 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2397 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Rooted Divided 55.9367 55.0794 1.01556
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Ranked Subtracted 220.682 221.472 0.79
importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Squared Divided 25703.8 27418.6 1.06671
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Rooted Subtracted 53.2692 52.3236 0.9456
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Ranked Divided 210.157 210.945 1.00375
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Squared Subtracted 54033.8 55375.5 1341.7
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Measured Divided 6707.29 6970.07 1.03918
2398 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted 3672.49 3482.34 190.15
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Ranked 220.682 221.472 0.79
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Measured Divided 6707.29 6970.07 1.03918
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Squared Subtracted 54033.8 55375.5 1341.7
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Rooted Divided 60.8344 61.7685 1.01535
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Subtracted 53.2692 52.3236 0.9456
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Ranked Divided 182.395 183.079 1.00375
r3h domain protein 1. [swissprot;acc:q15032] Squared 26296.9 28047.6 1.06657
2399 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] Measured Subtracted 7002.3 7192.25 189.95
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Ranked 220.682 221.471 0.789
homeobox protein otx1. [swissprot;acc:p32242] Measured Divided 5691.1 5913.92 1.03915
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Squared 25712.1 27419 1.06639
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Rooted Subtracted 53.2692 52.3236 0.9456
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Ranked Divided 182.4 183.083 1.00374
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Rooted 60.8344 61.7685 1.01535
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Squared Subtracted 13729.5 15069.8 1340.3
2400 helicase (fragment). [sptrembl;acc:q92771] Measured 7002.03 7191.88 189.85
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Divided 4368.44 4539.34 1.03912
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Rooted Subtracted 53.2692 52.3236 0.9456
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 60.8344 61.7685 1.01535
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Ranked 182.4 183.083 1.00374
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Squared 26996.7 28788.6 1.06637
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Ranked Subtracted 210.157 210.945 0.788
wd repeat domain 26. [refseq;acc:nm_025160] Squared 32575.7 33907 1331.3
2401 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Rooted 58.6893 57.7518 0.9375
60s ribosomal protein l19. [swissprot;acc:p14118] Measured 3687.49 3499.2 188.29
cone-rod homeobox protein. [swissprot;acc:o43186] Divided 5694.04 5916.78 1.03912
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Squared Subtracted 15961.5 17283.3 1321.8
oxidation resistance 1. [refseq;acc:nm_181354] Divided 26996.7 28788.6 1.06637
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Rooted 60.8344 61.7685 1.01535
serpin b12. [swissprot;acc:q96p63] Ranked Subtracted 218.2 218.984 0.784
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Divided 182.4 183.083 1.00374
2402 40s ribosomal protein s21. [swissprot;acc:p35265] Rooted Subtracted 58.6893 57.7518 0.9375
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Measured Divided 5078.5 5275.76 1.03884
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Rooted 60.8344 61.7685 1.01535
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Ranked 182.4 183.083 1.00374
lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Squared 26996.7 28788.6 1.06637
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Ranked Subtracted 218.2 218.984 0.784
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Measured 5978.83 6166.89 188.06
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Squared 15953.5 17274.8 1321.3
2403 40s ribosomal protein s21. [swissprot;acc:p35265] Measured Divided 5078.5 5275.76 1.03884
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Ranked 182.4 183.083 1.00374
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Rooted Subtracted 58.6893 57.7518 0.9375

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/