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 red Interaction Map Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
Interaction Map
green
network_comparison
401 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked Subtracted 254.434 High confidence 236.224 18.21
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 5794
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided 45694.9 Low confidence 42750.3 1.06888
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked 207.908 High confidence 226.218 1.08807
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 200.057 Low confidence 192.938 7.119
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted Divided 116.707 High confidence 106.044 1.10055
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Ranked 205.017 Low confidence 197.863 1.03616
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Rooted 75.7395 79.3703 1.04794
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 55.9231 High confidence 62.0565 6.1334
402 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Measured 8730.02 Low confidence 9159.19 429.17
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 High confidence 7168.2 937.26
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Squared Divided 48608.6 Low confidence 45485.7 1.06866
cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Rooted 75.7377 79.3677 1.04793
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 High confidence 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Subtracted 28190.4 33984.1 5793.7
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Rooted 70.0201 Low confidence 73.4927 3.4726
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 High confidence 249.983 18.181
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Divided 5201.41 4479.76 1.16109
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Subtracted 59.5128 65.604 6.0912
rab11-family interacting protein 4. [refseq;acc:nm_032932] Squared 34469.6 Low confidence 37645.4 3175.8
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Divided 207.908 High confidence 226.218 1.08807
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Measured 7934.21 Low confidence 8352.26 1.05269
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Ranked Subtracted 210.292 203.181 7.111
x-linked protein sts1769. [swissprot;acc:q99871] Divided 211.253 203.883 1.03615
403 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared Subtracted 28190.4 High confidence 33984.1 5793.7
calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 6.0912
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 72.2945 Low confidence 75.765 3.4705
eferin. [swissprot;acc:o75154] Squared 34469.6 37645.4 3175.8
elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Rooted Divided 70.3162 73.6827 1.04788
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 5201.41 High confidence 4479.76 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked Subtracted 228.468 246.338 17.87
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 7398.26 Low confidence 7826.48 428.22
Rooted Divided 59.6834 High confidence 65.6741 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured Subtracted 6259.3 7190.91 931.61
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Ranked 200.049 Low confidence 192.942 7.107
prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147] Squared Divided 48608.6 45485.7 1.06866
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Measured 8853.13 9319.56 1.05269
three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166] Ranked 211.253 203.883 1.03615
404 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 26819.1 High confidence 32855.4 1.22507
adiponectin receptor 2. [refseq;acc:nm_024551] Measured Subtracted 7170.39 Low confidence 7598.55 428.16
alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 High confidence 33984.1 5793.7
atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201] Divided 52108.1 Low confidence 48765.3 1.06855
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked Subtracted 228.463 High confidence 246.33 17.867
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 65.604 6.0912
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Divided 72.2476 Low confidence 75.7022 1.04782
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 High confidence 226.218 1.08807
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured Subtracted 7802.31 8731.82 929.51

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/