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 813 to 862 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
407 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Subtracted 1836.76 907.741 929.019
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided 6603.41 7664.65 1.16071
408 dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Subtracted 1836.76 907.763 928.997
409 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Divided 6102.59 7081.46 1.1604
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Subtracted 1836.76 907.774 928.986
410 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 928.92
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Divided 6102.59 7081.46 1.1604
411 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Subtracted 1836.8 907.903 928.897
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Divided 6102.59 7081.46 1.1604
412 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Subtracted 1836.81 907.978 928.832
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 3594.31 4169.95 1.16015
413 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Subtracted 1836.81 907.978 928.832
vav proto-oncogene. [swissprot;acc:p15498] Divided 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
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Subtracted 5051.16 5975.51 924.35
415 j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 7725.1 8647.74 922.64
vav-3 protein. [swissprot;acc:q9ukw4] Divided 6647.43 7706.18 1.15927
416 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Subtracted 7725.1 8647.74 922.64
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Divided 4509.54 5223.95 1.15842
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] 4522.71 5233.14 1.15708
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Subtracted 7725.1 8647.74 922.64
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Divided 5493.1 6350.19 1.15603
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Subtracted 7725.1 8647.74 922.64
419 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] Divided 5493.1 6350.19 1.15603
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Subtracted 5039.63 5961.83 922.2
420 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Divided 10235.2 11830.8 1.15589
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Subtracted 5942.49 6853.15 910.66
421 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 6739.43 7644.55 905.12
vav-2 protein. [swissprot;acc:p52735] Divided 6660.02 7697.78 1.15582
422 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Subtracted 460 1365 905
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Divided 5206.9 6010.04 1.15425
423 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Subtracted 6739.61 7644.58 904.97
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Divided 5207.03 6010.1 1.15423
424 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 6739.63 7644.59 904.96
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Divided 5207.78 6010.45 1.15413
425 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Subtracted 6739.7 7644.6 904.9
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 3729.02 4301.58 1.15354
426 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Subtracted 6739.81 7644.62 904.81
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Divided 5942.49 6853.15 1.15325
427 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 6739.81 7644.62 904.81
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Divided 11736.6 13531.9 1.15297
428 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Subtracted 6739.82 7644.63 904.81
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided 3721.19 4288.17 1.15237
429 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Subtracted 6739.81 7644.62 904.81
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Divided 6272.91 7226.06 1.15195
430 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Subtracted 6739.82 7644.63 904.81
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Divided 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
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Subtracted 6739.82 7644.63 904.81

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/