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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type description 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
Value Type
description
Network Comparison Type
red
green
network_comparison
2397 Measured yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Divided 6707.29 6970.07 1.03918
Ranked histone deacetylase 4 (hd4). [swissprot;acc:p56524] Subtracted 220.682 221.472 0.79
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Divided 210.157 210.945 1.00375
Squared importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] 25703.8 27418.6 1.06671
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Subtracted 54033.8 55375.5 1341.7
Rooted dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Divided 55.9367 55.0794 1.01556
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Subtracted 53.2692 52.3236 0.9456
2398 Measured 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] 3672.49 3482.34 190.15
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Divided 6707.29 6970.07 1.03918
Ranked histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Subtracted 220.682 221.472 0.79
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Divided 182.395 183.079 1.00375
Squared large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted 54033.8 55375.5 1341.7
r3h domain protein 1. [swissprot;acc:q15032] Divided 26296.9 28047.6 1.06657
Rooted mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 60.8344 61.7685 1.01535
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Subtracted 53.2692 52.3236 0.9456
2399 Measured 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] 7002.3 7192.25 189.95
homeobox protein otx1. [swissprot;acc:p32242] Divided 5691.1 5913.92 1.03915
Ranked histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Subtracted 220.682 221.471 0.789
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Divided 182.4 183.083 1.00374
Squared karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] 25712.1 27419 1.06639
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Subtracted 13729.5 15069.8 1340.3
Rooted map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] 53.2692 52.3236 0.9456
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Divided 60.8344 61.7685 1.01535
2400 Measured helicase (fragment). [sptrembl;acc:q92771] Subtracted 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
Ranked peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 182.4 183.083 1.00374
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Subtracted 210.157 210.945 0.788
Squared sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Divided 26996.7 28788.6 1.06637
wd repeat domain 26. [refseq;acc:nm_025160] Subtracted 32575.7 33907 1331.3
Rooted meiotic recombination protein spo11. [swissprot;acc:q9y5k1] 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
2401 Measured 60s ribosomal protein l19. [swissprot;acc:p14118] Subtracted 3687.49 3499.2 188.29
cone-rod homeobox protein. [swissprot;acc:o43186] Divided 5694.04 5916.78 1.03912
Ranked serpin b12. [swissprot;acc:q96p63] 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
Squared lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Subtracted 15961.5 17283.3 1321.8
oxidation resistance 1. [refseq;acc:nm_181354] Divided 26996.7 28788.6 1.06637
Rooted 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] Subtracted 58.6893 57.7518 0.9375
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Divided 60.8344 61.7685 1.01535
2402 Measured 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] 5078.5 5275.76 1.03884
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 5978.83 6166.89 188.06
Ranked 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] Divided 182.4 183.083 1.00374
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Subtracted 218.2 218.984 0.784
Squared lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Divided 26996.7 28788.6 1.06637
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Subtracted 15953.5 17274.8 1321.3
Rooted 40s ribosomal protein s21. [swissprot;acc:p35265] 58.6893 57.7518 0.9375
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Divided 60.8344 61.7685 1.01535
2403 Measured 40s ribosomal protein s21. [swissprot;acc:p35265] 5078.5 5275.76 1.03884
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Subtracted 5978.83 6166.89 188.06
Ranked cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Divided 182.4 183.083 1.00374

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/