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 818 to 867 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
409 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 0 219.19 227.308 1.03704
410 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 1 6102.59 7081.46 1.1604
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 0 218.71 226.81 1.03704
411 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 31122 30022.4 1.03663
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 1 6102.59 7081.46 1.1604
412 60s ribosomal protein l39. [swissprot;acc:p02404] 0 3024.78 2923.92 1.03449
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 1 3594.31 4169.95 1.16015
413 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 0 613.385 634.192 1.03392
vav proto-oncogene. [swissprot;acc:p15498] 1 6644.99 7707.8 1.15994
414 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 0 7520.78 7276.12 1.03363
415 vav-3 protein. [swissprot;acc:q9ukw4] 1 6647.43 7706.18 1.15927
zinc finger protein 232. [swissprot;acc:q9uny5] 0 721.814 699.215 1.03232
416 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 1 4509.54 5223.95 1.15842
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 721.888 699.297 1.03231
417 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 1 4522.71 5233.14 1.15708
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 0 721.913 699.324 1.0323
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 1 5493.1 6350.19 1.15603
zinc finger imprinted 2. [swissprot;acc:q9nzv7] 0 722.144 699.577 1.03226
419 60s ribosomal protein l18a. [swissprot;acc:q02543] 2688.7 2604.71 1.03225
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 1 5493.1 6350.19 1.15603
420 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 10235.2 11830.8 1.15589
trinucleotide repeat containing 15. [refseq;acc:nm_015575] 0 18889 19496 1.03214
421 importin 4. [refseq;acc:nm_024658] 491.926 476.639 1.03207
vav-2 protein. [swissprot;acc:p52735] 1 6660.02 7697.78 1.15582
422 kappa b-ras 1. [refseq;acc:nm_020345] 0 1153.15 1117.36 1.03203
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 1 5206.9 6010.04 1.15425
423 fibrillin 3. [refseq;acc:nm_032447] 0 14246 13809 1.03165
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 1 5207.03 6010.1 1.15423
424 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 0 3967.18 4091.59 1.03136
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 1 5207.78 6010.45 1.15413
425 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 0 2070.81 2134.56 1.03079
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 1 3729.02 4301.58 1.15354
426 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 5942.49 6853.15 1.15325
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 0 2071.59 2133.83 1.03004
427 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1195.87 1161.29 1.02978
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 1 11736.6 13531.9 1.15297
428 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 0 14267.5 14688.8 1.02953
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 1 3721.19 4288.17 1.15237
429 tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 0 472.351 485.852 1.02858
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 1 6272.91 7226.06 1.15195
430 succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 0 10247.8 10535 1.02803
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1 3804.09 4379.37 1.15123
431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 1.15102
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 146.622 150.709 1.02787
432 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 100.5 103.25 1.02736
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 1 5244.71 6036.27 1.15093
433 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 5244.88 6036.38 1.15091
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 0 100.5 103.25 1.02736
434 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 201 206.5

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/