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 Value Type green description Network Comparison Type Interaction Map network_comparison Filtered red
Results: HTML CSV LaTeX Showing element 601 to 650 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
green
description
Network Comparison Type
Interaction Map
network_comparison
red
151 46 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided High confidence 1.19565 55
179.639 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted Low confidence 12.049 191.688
194.554 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Divided 1.06148 206.516
198.444 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted High confidence 28.138 226.582
152 46 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided 1.19565 55
191.187 high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 1.06144 202.934
198.444 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Subtracted High confidence 28.138 226.582
199.761 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Low confidence 12.047 211.808
153 172.702 rab11-family interacting protein 4. [refseq;acc:nm_032932] Divided 1.06119 183.27
194.554 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Subtracted 11.962 206.516
198.444 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] High confidence 28.138 226.582
298.263 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided 1.19466 249.663
154 172.702 eferin. [swissprot;acc:o75154] Low confidence 1.06119 183.27
194.554 cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Subtracted 11.962 206.516
199.458 musashi 2 isoform a. [refseq;acc:nm_138962] High confidence 28.033 227.491
298.263 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided 1.19466 249.663
155 199.458 musashi 1. [refseq;acc:nm_002442] Subtracted 28.033 227.491
199.734 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Divided Low confidence 1.0605 211.818
209.795 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted 11.883 221.678
298.263 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided High confidence 1.19466 249.663
156 199.458 nuclear protein ukp68. [refseq;acc:nm_024824] Subtracted 28.033 227.491
199.761 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Divided Low confidence 1.06031 211.808
208.064 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted 11.825 219.889
298.263 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 High confidence 1.19466 249.663
157 168.371 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 1.0602 178.507
191.187 high-mobility group 20a. [refseq;acc:nm_018200] Subtracted 11.747 202.934
284 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 28 312
298.263 transcription factor lbx1. [swissprot;acc:p52954] Divided 1.19466 249.663
158 205.073 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted Low confidence 11.723 216.796
207.417 dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Divided 1.05988 219.838
284 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Subtracted High confidence 28 312
298.263 mosaic protein lgn. [swissprot;acc:p81274] Divided 1.19466 249.663
159 205.07 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Subtracted Low confidence 11.72 216.79
207.417 c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Divided 1.05988 219.838
284 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted High confidence 28 312
298.263 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided 1.19466 249.663
160 205.066 proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted Low confidence 11.717 216.783
235.538 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Divided 1.0595 222.31
284 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted High confidence 28 312
298.263 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided 1.19466 249.663
161 207.907 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted Low confidence 11.693 219.6
235.547 adenomatous polyposis coli like. [refseq;acc:nm_005883] Divided 1.0594 222.34
284 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted High confidence 28 312
298.263 rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Divided 1.19466 249.663
162 170 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Subtracted 28 142
186.913 defender against cell death 1 (dad-1). [swissprot;acc:p46966] Divided Low confidence 1.05926 197.99
207.903 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 11.69 219.593
249.187 nostrin. [refseq;acc:nm_052946] Divided High confidence 1.19058 209.299
163 105 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted 28 133
191.393 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Divided Low confidence 1.05907 202.698

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/