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 12864 to 12913 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
1608 ubiquitin. [swissprot;acc:p02248] Measured High confidence 6158.22 6597.55 1.07134
1609 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44
dual specificity protein phosphatase 13 (ec 3.1.3.48) (ec 3.1.3.16) (testis- and skeletal-muscle-specific dsp). [swissprot;acc:q9uii6] Ranked Low confidence 199.691 195.607 1.02088
heat shock factor protein 4 (hsf 4) (heat shock transcription factor 4) (hstf 4) (hhsf4). [swissprot;acc:q9ulv5] Measured 8141.75 8415.33 1.0336
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Rooted High confidence 65.5919 67.884 1.03494
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Squared Low confidence 46189.9 44295.3 1.04277
splicing factor, arginine/serine-rich 6 (pre-mrna splicing factor srp55). [swissprot;acc:q13247] Rooted 71.6217 74.2075 1.0361
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Ranked High confidence 208.113 204.876 1.0158
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Squared 28992.5 32145.6 1.10876
1610 eif-5a2 protein. [refseq;acc:nm_020390] Measured 6222.4 6665.83 1.07126
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Squared 15639.2 17338.5 1.10866
ikappab kinase complex-associated protein (ikk complex-associated protein) (p150). [swissprot;acc:o95163] Measured Low confidence 7843.41 8106.95 1.0336
mus81 endonuclease. [refseq;acc:nm_025128] Ranked 195.31 191.317 1.02087
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Rooted High confidence 67.4766 69.831 1.03489
splicing factor, arginine/serine-rich 4 (pre-mrna splicing factor srp75) (srp001lb). [swissprot;acc:q08170] Low confidence 71.6217 74.2075 1.0361
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Ranked High confidence 208.122 204.886 1.01579
vps10 domain-containing receptor sorcs2 precursor. [swissprot;acc:q96pq0] Squared Low confidence 51308.3 49204.2 1.04276
1611 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Measured High confidence 5497.73 5132.35 1.07119
heat shock factor binding protein 1. [swissprot;acc:o75506] Squared 27263.5 30225.7 1.10865
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Rooted 67.4958 69.8487 1.03486
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Measured Low confidence 7703.86 7962.64 1.03359
my016 protein. [sptrembl;acc:q9h3k6] Rooted 73.8923 76.5593 1.03609
p10-binding protein. [refseq;acc:nm_024491] Ranked High confidence 221.313 217.877 1.01577
similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 195.31 191.317 1.02087
vps10 domain-containing receptor sorcs3 precursor. [swissprot;acc:q9upu3] Squared 51308.3 49204.2 1.04276
1612 brain protein 16. [refseq;acc:nm_016458] High confidence 26202.2 29043.8 1.10845
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Ranked 221.426 224.902 1.0157
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Measured 6212.98 6655.12 1.07116
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Ranked Low confidence 195.31 191.317 1.02087
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Rooted High confidence 67.5045 69.8568 1.03485
sortilin-related receptor precursor (sorting protein-related receptor containing ldlr class a repeats) (sorla) (sorla-1) (low-density lipoprotein receptor relative with 11 ligand-binding repeats) (ldlr relative with 11 ligand-binding repeats) (lr11). [swissprot;acc:q92673] Squared Low confidence 51308.3 49204.2 1.04276
splicing factor 1; zinc finger protein 162. [refseq;acc:nm_004630] Rooted 72.2859 74.8944 1.03609
zinc finger protein 277. [swissprot;acc:q9nrm2] Measured 7691.32 7949.57 1.03358
1613 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Ranked High confidence 182.378 185.241 1.0157
igf-ii mrna-binding protein 1. [refseq;acc:nm_006546] Measured Low confidence 7815.17 8077.42 1.03356
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] High confidence 6035.6 6464.5 1.07106
mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5] Rooted Low confidence 69.7446 72.2614 1.03609
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Ranked 192.787 188.847 1.02086
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Squared High confidence 15399.5 17067.9 1.10834
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Rooted 67.511 69.8628 1.03484
vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21] Squared Low confidence 51308.3 49204.2 1.04276
1614 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Rooted 70.2663 72.8023 1.03609
hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Ranked High confidence 217.233 213.897 1.0156
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Measured 6035.6 6464.5 1.07106
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Squared 15399.5 17067.9 1.10834
ras-related protein rab-5a. [swissprot;acc:p20339] Measured Low confidence 7968.53 8235.92 1.03356
ras-related protein rap-2b. [swissprot;acc:p17964] Ranked 202.026 197.9 1.02085
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Squared 43732.3 41938.9 1.04276
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted High confidence 54.1932 56.0802 1.03482
1615 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Ranked Low confidence 205.179 200.988 1.02085

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/