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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Network Comparison Type Value Type Interaction Map green Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
green
network_comparison
red
401 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Subtracted Ranked High confidence 236.224 18.21 254.434
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 33982.7 5794 28188.7
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided Low confidence 42750.3 1.06888 45694.9
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 High confidence 226.218 1.08807 207.908
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted Low confidence 192.938 7.119 200.057
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] Divided Rooted High confidence 106.044 1.10055 116.707
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 Low confidence 197.863 1.03616 205.017
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Rooted 79.3703 1.04794 75.7395
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted High confidence 62.0565 6.1334 55.9231
402 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Measured Low confidence 9159.19 429.17 8730.02
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 7168.2 937.26 6230.94
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Divided Squared Low confidence 45485.7 1.06866 48608.6
cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Rooted 79.3677 1.04793 75.7377
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared High confidence 48393.1 1.22601 39472
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 55.2294 1.10037 50.1918
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Subtracted Squared 33984.1 5793.7 28190.4
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Rooted Low confidence 73.4927 3.4726 70.0201
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked High confidence 249.983 18.181 231.802
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided Measured 4479.76 1.16109 5201.41
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Subtracted Rooted 65.604 6.0912 59.5128
rab11-family interacting protein 4. [refseq;acc:nm_032932] Squared Low confidence 37645.4 3175.8 34469.6
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Divided Ranked High confidence 226.218 1.08807 207.908
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 Low confidence 8352.26 1.05269 7934.21
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted Ranked 203.181 7.111 210.292
x-linked protein sts1769. [swissprot;acc:q99871] Divided 203.883 1.03615 211.253
403 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Subtracted Squared High confidence 33984.1 5793.7 28190.4
calcyphosine. [swissprot;acc:q13938] Rooted 65.604 6.0912 59.5128
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Low confidence 75.765 3.4705 72.2945
eferin. [swissprot;acc:o75154] Squared 37645.4 3175.8 34469.6
elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Divided Rooted 73.6827 1.04788 70.3162
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured High confidence 4479.76 1.16109 5201.41
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 48362.1 1.22548 39463.9
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Subtracted Ranked 246.338 17.87 228.468
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided Rooted 65.6741 1.10037 59.6834
Subtracted Measured Low confidence 7826.48 428.22 7398.26
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Divided Ranked High confidence 226.218 1.08807 207.908
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Subtracted Measured 7190.91 931.61 6259.3
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Ranked Low confidence 192.942 7.107 200.049
prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147] Divided Squared 45485.7 1.06866 48608.6
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Measured 9319.56 1.05269 8853.13
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 203.883 1.03615 211.253
404 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared High confidence 32855.4 1.22507 26819.1
adiponectin receptor 2. [refseq;acc:nm_024551] Subtracted Measured Low confidence 7598.55 428.16 7170.39
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 High confidence 33984.1 5793.7 28190.4
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 Low confidence 48765.3 1.06855 52108.1
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] Subtracted Ranked High confidence 246.33 17.867 228.463
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 65.604 6.0912 59.5128
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Divided Low confidence 75.7022 1.04782 72.2476
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked High confidence 226.218 1.08807 207.908
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted Measured 8731.82 929.51 7802.31

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/