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 3558 to 3607 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
890 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Squared 18178.2 21081.9 1.15974
syntaxin 7. [swissprot;acc:o15400] Ranked 217.181 209.012 1.03908
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Measured 5350.87 5896.82 1.10203
891 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 5385.04 5933.65 1.10188
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Rooted 56.7818 60.2369 1.06085
rw1 protein (fragment). [swissprot;acc:q92545] Squared 18178.2 21081.9 1.15974
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Ranked 212.028 204.055 1.03907
892 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Rooted 56.7817 60.2369 1.06085
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Measured 6784.67 7475.48 1.10182
di-ras2. [refseq;acc:nm_017594] Ranked 212.028 204.055 1.03907
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Squared 26312 30514.1 1.1597
893 e-1 enzyme. [refseq;acc:nm_021204] Measured 6603.09 7274.72 1.10171
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Rooted 56.781 60.2344 1.06082
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Ranked 227.585 219.037 1.03903
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Squared 26312 30514.1 1.1597
894 parafibromin. [refseq;acc:nm_024529] Measured 4331.17 4771.22 1.1016
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Ranked 217.491 209.323 1.03902
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Squared 20322.5 23567.1 1.15966
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Rooted 56.2142 59.6282 1.06073
895 exocyst complex component sec8. [swissprot;acc:q96a65] 63.2983 67.1422
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured 10247.8 11289 1.1016
leucyl-trna synthetase. [refseq;acc:nm_020117] Squared 21830.4 25308.2 1.15931
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Ranked 217.491 209.323 1.03902
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 230.811 239.785 1.03888
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Squared 21830.4 25308.3 1.15931
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Measured 5208.27 5737.17 1.10155
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Rooted 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
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 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
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked 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
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Squared 21156.1 24524.1 1.1592
899 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 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
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Ranked 229.171 238.048 1.03874
900 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Measured 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
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Ranked 229.171 238.048 1.03874
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Squared 28068.5 32522.9 1.1587
901 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Rooted 66.5785 70.6139 1.06061
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Measured 5929.61 6531.55 1.10151
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] Ranked 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
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Ranked 237.62 228.762 1.03872
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured 10246.1 11285.8 1.10147

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/