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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 743 to 792 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
372 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 0 5427.25 5130.58 1.05782
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 1 5067 5926.17 1.16956
373 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 0 2713.5 2864.68 1.05571
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 1 5066.99 5926.1 1.16955
374 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 0 2323.8 2452.23 1.05527
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 1 5066.93 5925.38 1.16942
375 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 2323.8 2452.23 1.05527
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 1 4700.42 5492.63 1.16854
376 44050 protein. [refseq;acc:nm_178832] 17385.9 14889.2 1.16769
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 0 4912.01 4658.69 1.05438
377 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 884.254 931.405 1.05332
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 1 17385.9 14889.2 1.16769
378 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 0 703.068 739.623 1.05199
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 1 12471.7 14561.7 1.16758
379 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 0 1927.62 1833.64 1.05125
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 1 6704.44 7811.45 1.16512
380 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 12998.5 15138.2 1.16461
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 0 1927.62 1833.64 1.05125
381 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 2509.05 2633.79 1.04972
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 1 5246.01 6109.31 1.16456
382 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 0 377.445 359.98 1.04852
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 1 4533.74 5279.4 1.16447
383 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 0 379.489 362.023 1.04825
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 1 4533.74 5279.4 1.16447
384 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 0 8243.06 8627.63 1.04665
385 40s ribosomal protein s28. [swissprot;acc:p25112] 387.486 405.367 1.04615
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 1 4533.74 5279.4 1.16447
386 60s ribosomal protein l8. [swissprot;acc:p25120]
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 0 2156.64 2254.12 1.0452
387 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1388.29 1330.37 1.04354
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 1 4533.74 5279.4 1.16447
388 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]
scratch; scratch 1. [refseq;acc:nm_031309] 0 1398.21 1339.9 1.04352
389 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 11512.3 12011.7 1.04338
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 1 4533.74 5279.4 1.16447
390 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 0 11512.3 12011.7 1.04338
rw1 protein (fragment). [swissprot;acc:q92545] 1 4533.74 5279.4 1.16447
391 seven in absentia homolog 1. [refseq;acc:nm_003031] 0 2221.04 2316.94 1.04318
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 3658.76 3144.39 1.16358
392 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 0 229.211 219.891 1.04238
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 1 3641.89 4236.95 1.16339
393 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 4490.28 5222.25 1.16301
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 0 2131.42 2218.51 1.04086
394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 1 4490.28 5222.25 1.16301
histone h2b.d (h2b/d). [swissprot;acc:q99877] 0 2131.52 2218.58 1.04084
395 histone h2b.s (h2b/s). [swissprot;acc:p57053] 2131.83 2218.82 1.04081
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 4532.73 5269.33 1.16251
396 histone h2b. [refseq;acc:nm_175055] 0 2131.91 2218.89 1.0408
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 1 6563.65 7627.29 1.16205

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/