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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1608 ubiquitin. [swissprot;acc:p02248] Measured Divided 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
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Ranked Subtracted 207.916 204.662 3.254
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Squared 24291.6 26802.4 2510.8
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 Divided 65.5919 67.884 1.03494
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 61.9701 64.1935 2.2234
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Measured 6297.05 6721.08 424.03
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Ranked Divided 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 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Ranked Subtracted 217.446 214.2 3.246
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Rooted 61.9701 64.1935 2.2234
eif-5a2 protein. [refseq;acc:nm_020390] Measured Divided 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
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Measured Subtracted 6079.19 6503.12 423.93
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Rooted Divided 67.4766 69.831 1.03489
tata element modulatory factor (tmf). [swissprot;acc:p82094] Squared Subtracted 23713.7 26223.8 2510.1
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 Divided 208.122 204.886 1.01579
1611 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Rooted Subtracted 61.9705 64.1938 2.2233
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Measured Divided 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
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Measured Subtracted 6079.19 6503.12 423.93
p10-binding protein. [refseq;acc:nm_024491] Ranked Divided 221.313 217.877 1.01577
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Squared Subtracted 23713.7 26223.8 2510.1
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Ranked 217.446 214.2 3.246
1612 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Measured 6079.19 6503.12 423.93
brain protein 16. [refseq;acc:nm_016458] Squared Divided 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
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Squared Subtracted 23713.7 26223.8 2510.1
pp1201 protein. [refseq;acc:nm_022152] Ranked 217.446 214.2 3.246
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Rooted Divided 67.5045 69.8568 1.03485
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Subtracted 61.9703 64.1936 2.2233
1613 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Measured 6079.19 6503.12 423.93
ammecr1 protein. [refseq;acc:nm_015365] Squared 23713.7 26223.8 2510.1
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 Divided 182.378 185.241 1.0157
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 217.446 214.2 3.246
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Measured Divided 6035.6 6464.5 1.07106
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Squared 15399.5 17067.9 1.10834
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Rooted Subtracted 61.9703 64.1936 2.2233
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Divided 67.511 69.8628 1.03484
1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Ranked 217.233 213.897 1.0156
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Squared Subtracted 23713.7 26223.8 2510.1
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Measured Divided 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
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Rooted Subtracted 61.9703 64.1936 2.2233
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Measured 6079.19 6503.12 423.93
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked 217.446 214.2 3.246
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted Divided 54.1932 56.0802 1.03482
1615 adaptor-associated kinase 1. [refseq;acc:nm_014911] Subtracted 61.9703 64.1936 2.2233

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/