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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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 [...,...].
Network Comparison Type Value Type green Gene description Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2051 to 2100 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
green
description
Rank
network_comparison
red
217.175 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] 1983 1.00955 219.25
217.193 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] 1986 1.00952 219.26
9 kda protein. [swissprot;acc:p13994] 1988
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 1984
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] 1985
217.194 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 1990 1.00951
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] 1991
217.195 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 1989 219.261
217.199 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 1470 1.0194 221.412
glutamyl trna synthetase. [sptrembl;acc:o14563] 1473
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] 1472
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] 1471
217.207 zasp protein (fragment). [sptrembl;acc:q9y4z3] 1992 1.00948 219.267
217.258 coactosin-like protein. [swissprot;acc:q14019] 1219 1.025 211.959
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 1218
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 1217
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 1221
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 1220
217.263 60s ribosomal protein l21. [swissprot;acc:p46778] 1054 1.03082 223.958
217.285 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 2474 1.00298 216.64
217.362 peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 1753 1.01256 220.091
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 1754
217.373 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 1884 1.01066 215.081
217.47 ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] 2109 1.00718 219.032
217.481 serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 1638 1.01474 220.686
217.511 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 2111 1.00706 219.047
217.533 2113 1.007 219.055
217.564 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] 2472 1.00301 218.218
217.571 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 2475 1.00298 218.219
217.574 enigma protein; lim domain protein. [refseq;acc:nm_005451] 1929 1.01001 219.753
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 1931
217.633 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] 2542 1.002 218.068
217.659 regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] 1972 1.00973 219.777
217.682 tensin. [refseq;acc:nm_022648] 2504 1.00255 218.238
217.699 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 1617 1.01537 221.045
217.704 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 1686 1.01399 220.75
217.739 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 383 1.09242 237.862
217.74 wd repeat domain 26. [refseq;acc:nm_025160] 1429 1.02057 213.351
217.75 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 1869 1.01082 220.107
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] 1870
217.801 lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] 2107 1.00727 216.23
217.82 ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 1933 1.00998 215.667
217.877 p10-binding protein. [refseq;acc:nm_024491] 1611 1.01577 221.313
217.922 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 1002 1.03325 225.167
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 1003
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 1001
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 1000
217.926 dpy-30-like protein. [swissprot;acc:q9c005] 1815 1.01164 220.462
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] 1817
neighbor of cox4. [swissprot;acc:o43402] 1818

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/