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 2027 to 2076 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked Subtracted 227.999 204.357 23.642
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured Divided 6417.18 7859.6 1.22477
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 1.12756
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 1.11569
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Squared Subtracted 59338.5 68268.3 8929.8
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 69165 52991.7 1.3052
255 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Subtracted 39472 48393.1 8921.1
mad protein (max dimerizer). [swissprot;acc:q05195] Measured 4455.95 5774.03 1318.08
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 23.633
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 200.691 179.88 1.11569
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted Subtracted 132.156 122.835 9.321
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured Divided 6417.18 7859.6 1.22477
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 62.9007 70.8854 1.12694
256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 132.114 122.802 9.312
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared Divided 15465.1 20151 1.303
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 39463.9 48362.1 8898.2
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured Divided 6417.19 7859.51 1.22476
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked Subtracted 227.999 204.37 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured 4456.67 5773.77 1317.1
Ranked Divided 227.999 204.357 1.11569
257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 51.6125 45.8409 1.12591
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured 6417.31 7858.12 1.22452
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Rooted Subtracted 132.467 123.158 9.309
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Ranked Divided 200.691 179.88 1.11569
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 15482.3 20162.4 1.30229
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Measured Subtracted 4456.93 5773.67 1316.74
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 8864.2
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked 242.14 265.697 23.557
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured Divided 6417.33 7857.93 1.22449
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 76438 58889.7 1.29799
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Measured Subtracted 4457.06 5773.63 1316.57
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked Divided 227.999 204.366 1.11564
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] Squared Subtracted 33522.8 42384.8 8862
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Rooted 132.063 122.761 9.302
thrombospondin 3 precursor. [swissprot;acc:p49746] Divided 51.6132 45.8422 1.12589
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked Subtracted 242.14 265.696 23.556
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Squared Divided 76360.8 58841.7 1.29773
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 227.999 204.37 1.11562
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured 6417.81 7852.52 1.22355
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] Squared Subtracted 33514.4 42370.8 8856.4
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Rooted 107.961 117.197 9.236
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Measured 4569.48 5885.79 1316.31
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted Divided 58.2964 65.5926 1.12516
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 219.421 196.978 1.11394
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Measured Subtracted 12515.4 11221.1 1294.3
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared Divided 76296.4 58801.6 1.29752
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 59.0951 66.4332 1.12417

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/