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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1323 to 1372 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
331 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 1 312 284 1.09859
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Subtracted 224.647 203.242 21.405
332 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 224.633 203.251 21.382
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 0 11634.4 10989.9 644.5
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 8125.5 7697.5 1.0556
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 1 312 284 1.09859
333 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 1 312 284 1.09859
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Subtracted 0 8095.69 8732.68 636.99
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 1 265.634 244.304 21.33
334 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 0 10253.5 9622.45 631.05
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 8125.5 7697.5 1.0556
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 312 284 1.09859
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Subtracted 232.473 211.207 21.266
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 312 284 1.09859
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Subtracted 223.273 202.423 20.85
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 0 8125.5 7697.5 1.0556
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 10897 11520 623
336 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 9270.49 8650.24 620.25
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Divided 1 312 284 1.09859
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 0 8125.5 7697.5 1.0556
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Subtracted 1 241.045 261.874 20.829
337 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 0 12953.2 12273.2 1.05541
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Subtracted 9431 8815 616
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 1 200.691 179.88 20.811
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Subtracted 0 13801.7 13185.9 615.8
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Divided 11149.7 10571.4 1.0547
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 1 200.691 179.88 20.811
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Divided 243.583 267.527 1.0983
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Subtracted 200.691 179.88 20.811
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 0 7163.55 7759.61 596.06
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Divided 10344.1 10903.3 1.05406
340 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Subtracted 1 239.75 260.544 20.794
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 0 8123.75 8719 595.25
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 11372.3 10792.3 1.05374
myelin gene expression factor 2. [refseq;acc:nm_016132] 1 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 0 8702.94 9169.98 1.05366
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 13652.7 13061 591.7
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 1 240.788 261.416 20.628
342 40s ribosomal protein s20. [swissprot;acc:p17075] Divided 243.5 267.21 1.09737
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Subtracted 0 11563.7 12151.8 588.1
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 1 240.913 261.45 20.537
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 0 10074 10609 1.05311
343 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted 10405.1 10992.4 587.3
casein kinase i alpha s-like. [refseq;acc:nm_145203] Divided 8356.31 8788.62 1.05173
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 1 241.625 265.136 1.0973
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 231.73 211.252 20.478

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/