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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4180 to 4229 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
red
green
network_comparison
523 histone h2b.c (h2b/c). [swissprot;acc:q99880] Subtracted Ranked 247.47 233.441 14.029
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Squared 31100.2 36086.5 4986.3
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided 53174 44377.4 1.19822
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted 66.377 72.2842 1.08899
zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 49.3451 54.4606 5.1155
524 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Divided Squared 53174 44377.4 1.19822
aquaporin 5. [swissprot;acc:p55064] Measured 10640 12117.6 1.13887
brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 1.08899
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 215.237 230.07 1.06891
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Subtracted 247.47 233.441 14.029
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Squared 31100.2 36086.5 4986.3
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted 49.3451 54.4606 5.1155
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured 5206.9 6010.04 803.14
525 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Divided Squared 53174 44377.4 1.19822
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Ranked 215.237 230.07 1.06891
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Subtracted Rooted 49.3451 54.4606 5.1155
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Ranked 247.47 233.441 14.029
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Divided Measured 10639.8 12117.3 1.13887
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Subtracted 5207.03 6010.1 803.07
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Divided Rooted 113.374 123.463 1.08899
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Subtracted Squared 31100.1 36086.4 4986.3
526 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Divided Measured 10639.9 12117.4 1.13886
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Subtracted Rooted 49.0882 54.2027 5.1145
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Divided Squared 31189.6 37352.8 1.1976
histone h2b. [refseq;acc:nm_175055] Subtracted Ranked 247.47 233.441 14.029
keratin associated protein 4.4. [refseq;acc:nm_032524] Squared 31100.2 36086.5 4986.3
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided Ranked 250.538 234.401 1.06884
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Subtracted Measured 5207.78 6010.45 802.67
septin 6. [swissprot;acc:q14141] Divided Rooted 113.169 123.23 1.0889
527 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Subtracted Squared 31100.1 36086.4 4986.3
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Divided Ranked 248.56 232.579 1.06871
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 1.08865
histone h2b.s (h2b/s). [swissprot;acc:p57053] Subtracted Ranked 247.47 233.441 14.029
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided Measured 4775.11 5438.18 1.13886
Subtracted Rooted 56.3798 61.4858 5.106
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 4700.42 5492.63 792.21
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided Squared 18011.9 21552.8 1.19659
528 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 12111.4 1.13879
histone h2b.d (h2b/d). [swissprot;acc:q99877] Subtracted Ranked 247.47 233.441 14.029
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured 5244.71 6036.27 791.56
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Rooted 55.1759 60.2621 5.0862
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Squared 31100.1 36086.4 4986.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Divided 10606 8868.81 1.19588
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Rooted 66.941 72.7546 1.08685
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked 222.146 237.393 1.06864
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Subtracted Rooted 55.1759 60.2621 5.0862
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked 247.47 233.441 14.029
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Squared 31100.1 36086.4 4986.3
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Divided Measured 8600.02 9792.49 1.13866

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/