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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Gene Value Type Rank Interaction Map description Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
276 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Divided 0 10817.1 12125.1 1.12092
gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 1 699.76 1894.39 1194.63
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 3119.98 2579.49 1.20953
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Subtracted 0 465.37 562.085 96.715
277 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Divided 870.93 975.647 1.12024
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Subtracted 143 47 96
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 1 8600.02 9792.49 1192.47
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Divided 3119.98 2579.49 1.20953
278 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Subtracted 8600.02 9792.49 1192.47
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Divided 0 2162.33 1932 1.11922
seven in absentia homolog 1. [refseq;acc:nm_003031] Subtracted 2221.04 2316.94 95.9
transcription factor lbx1. [swissprot;acc:p52954] Divided 1 3119.98 2579.49 1.20953
279 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 0 545.902 610.424 1.11819
mosaic protein lgn. [swissprot;acc:p81274] 1 3119.98 2579.49 1.20953
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Subtracted 0 184.422 88.5622 95.8598
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 1 4771.21 5961.43 1190.22
280 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 0 578.056 482.7 95.356
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Divided 545.902 610.424 1.11819
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Subtracted 1 677.5 1865.5 1188
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided 3119.98 2579.49 1.20953
281 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Subtracted 0 1927.62 1833.64 93.98
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided 1 3119.98 2579.49 1.20953
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Subtracted 677.5 1865.5 1188
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Divided 0 545.902 610.424 1.11819
282 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Subtracted 1927.62 1833.64 93.98
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Divided 178.955 199.751 1.11621
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Subtracted 1 677.5 1865.5 1188
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Divided 3119.98 2579.49 1.20953
283 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Subtracted 677.5 1865.5 1188
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Divided 0 841.301 753.849 1.11601
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 1 5221.28 6314.35 1.20935
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Subtracted 0 197.333 290.667 93.334
284 60s ribosomal protein l15. [swissprot;acc:p39030] 846.216 753.793 92.423
60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided 1753.85 1956.36 1.11547
paxillin. [swissprot;acc:p49023] 1 5221.28 6314.35 1.20935
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 677.5 1865.5 1188
285 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 0 2698.62 3010.22 1.11547
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 1 4068.56 5252.6 1184.04
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 23326.5 19296.4 1.20885
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 0 5699.32 5607.7 91.62
286 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Divided 5497.01 6127.24 1.11465
exocyst complex component sec5. [swissprot;acc:q96kp1] 1 23316 19288.8 1.20878
rna-binding protein. [refseq;acc:nm_019027] Subtracted 4069.83 5252.17 1182.34
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] 0 939 848 91
287 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Divided 726.245 808.929 1.11385
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 1 4069.83 5252.17 1182.34
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Divided 23303.1 19279.5 1.2087
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 0 2363.32 2454.04 90.72
288 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Divided 1 23422.4 19380.3 1.20857
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 0 1293.73 1161.64 1.11371

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/