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 red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 601 to 650 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
151 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Divided Low confidence 206.516 1.06148 194.554
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted 191.688 12.049 179.639
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided High confidence 55 1.19565 46
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted 226.582 28.138 198.444
152 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Low confidence 211.808 12.047 199.761
high-mobility group 20a. [refseq;acc:nm_018200] Divided 202.934 1.06144 191.187
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 55 1.19565 46
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Subtracted 226.582 28.138 198.444
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided 249.663 1.19466 298.263
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 226.582 28.138 198.444
rab11-family interacting protein 4. [refseq;acc:nm_032932] Divided Low confidence 183.27 1.06119 172.702
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Subtracted 206.516 11.962 194.554
154 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]
eferin. [swissprot;acc:o75154] Divided 183.27 1.06119 172.702
musashi 2 isoform a. [refseq;acc:nm_138962] Subtracted High confidence 227.491 28.033 199.458
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided 249.663 1.19466 298.263
155 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Low confidence 211.818 1.0605 199.734
musashi 1. [refseq;acc:nm_002442] Subtracted High confidence 227.491 28.033 199.458
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 249.663 1.19466 298.263
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted Low confidence 221.678 11.883 209.795
156 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Divided 211.808 1.06031 199.761
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted 219.889 11.825 208.064
nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 227.491 28.033 199.458
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Divided 249.663 1.19466 298.263
157 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 178.507 1.0602 168.371
high-mobility group 20a. [refseq;acc:nm_018200] Subtracted 202.934 11.747 191.187
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 312 28 284
transcription factor lbx1. [swissprot;acc:p52954] Divided 249.663 1.19466 298.263
158 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Subtracted 312 28 284
dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Divided Low confidence 219.838 1.05988 207.417
mosaic protein lgn. [swissprot;acc:p81274] High confidence 249.663 1.19466 298.263
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted Low confidence 216.796 11.723 205.073
159 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 216.79 11.72 205.07
c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Divided 219.838 1.05988 207.417
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted High confidence 312 28 284
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided 249.663 1.19466 298.263
160 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Low confidence 222.31 1.0595 235.538
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] High confidence 249.663 1.19466 298.263
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 312 28 284
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Low confidence 216.783 11.717 205.066
161 adenomatous polyposis coli like. [refseq;acc:nm_005883] Divided 222.34 1.0594 235.547
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 219.6 11.693 207.907
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence 312 28 284
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Divided 249.663 1.19466 298.263
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Subtracted 142 28 170
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Divided Low confidence 197.99 1.05926 186.913
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 219.593 11.69 207.903
nostrin. [refseq;acc:nm_052946] Divided High confidence 209.299 1.19058 249.187
163 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted 133 28 105
eap30 subunit of ell complex. [refseq;acc:nm_007241] Divided 209.299 1.19058 249.187

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/