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 7162 to 7211 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
896 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared Subtracted 23242.1 26955.1 3713
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Divided 21830.4 25308.3 1.15931
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted Subtracted 73.8603 77.5904 3.7301
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 5167.88 4594.43 573.45
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 5208.27 5737.17 1.10155
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked Subtracted 243.34 235.322 8.018
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Rooted Divided 56.2142 59.6282 1.06073
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Ranked 272.878 283.472 1.03882
exocyst complex component sec15a. [swissprot;acc:q8tag9] Measured Subtracted 6201.54 6774.35 572.81
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Squared Divided 29924.3 34690.9 1.15929
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 5929.48 6531.48 1.10153
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Rooted 56.2142 59.6282 1.06073
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Subtracted 73.8553 77.585 3.7297
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Ranked 210.863 218.878 8.015
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Squared 23242.1 26955.1 3713
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked Divided 229.171 238.048 1.03874
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Measured 5929.55 6531.52 1.10152
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Rooted 56.2142 59.6282 1.06073
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Measured Subtracted 5859.25 6432.03 572.78
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] Ranked 210.863 218.878 8.015
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Rooted 61.6325 65.3619 3.7294
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Squared Divided 21156.1 24524.1 1.1592
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Subtracted 23242.1 26955.1 3713
899 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 29345.7 34004.2 1.15875
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Rooted 66.5785 70.6139 1.06061
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Measured 5929.55 6531.52 1.10152
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 5859.25 6432.03 572.78
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Ranked 212.027 204.05 7.977
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Rooted 73.8426 77.5711 3.7285
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Squared 22587.2 26296.1 3708.9
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Ranked Divided 229.171 238.048 1.03874
900 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 212.028 204.053 7.975
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Measured Divided 4713.58 4279.17 1.10152
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Rooted 66.5785 70.6139 1.06061
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Measured Subtracted 5859.25 6432.03 572.78
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Rooted 51.1896 47.4617 3.7279
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Squared 28335.4 32042.6 3707.2
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Ranked Divided 229.171 238.048 1.03874
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Squared 28068.5 32522.9 1.1587
901 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Rooted Subtracted 51.7081 47.9816 3.7265
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Squared Divided 28068.5 32522.9 1.1587
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Measured Subtracted 6080.91 6653.52 572.61
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Rooted Divided 66.5785 70.6139 1.06061
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Measured 5929.61 6531.55 1.10151
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared Subtracted 22017.1 25721.9 3704.8
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Ranked 212.028 204.055 7.973
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Divided 237.62 228.762 1.03872
902 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Squared 28068.5 32522.9 1.1587
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Rooted Subtracted 62.309 58.5957 3.7133
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Ranked Divided 237.62 228.762 1.03872

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/