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 Value Type description Network Comparison Type Interaction Map 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
Value Type
description
Network Comparison Type
red
green
network_comparison
1608 Rooted likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided 99.0527 95.6982 1.03505
1609 Measured 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44 1.07134
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Subtracted 6297.05 6721.08 424.03
Ranked apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 204.662 3.254
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 208.113 204.876 1.0158
Squared eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Subtracted 24291.6 26802.4 2510.8
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Divided 28992.5 32145.6 1.10876
Rooted 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] 65.5919 67.884 1.03494
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 61.9701 64.1935 2.2234
1610 Measured eif-5a2 protein. [refseq;acc:nm_020390] Divided 6222.4 6665.83 1.07126
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted 6079.19 6503.12 423.93
Ranked c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 214.2 3.246
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] Divided 208.122 204.886 1.01579
Squared hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 15639.2 17338.5 1.10866
tata element modulatory factor (tmf). [swissprot;acc:p82094] Subtracted 23713.7 26223.8 2510.1
Rooted clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 61.9701 64.1935 2.2234
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Divided 67.4766 69.831 1.03489
1611 Measured cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 5497.73 5132.35 1.07119
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Subtracted 6079.19 6503.12 423.93
Ranked p10-binding protein. [refseq;acc:nm_024491] Divided 221.313 217.877 1.01577
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 217.446 214.2 3.246
Squared heat shock factor binding protein 1. [swissprot;acc:o75506] Divided 27263.5 30225.7 1.10865
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] Subtracted 23713.7 26223.8 2510.1
Rooted arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 61.9705 64.1938 2.2233
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 67.4958 69.8487 1.03486
1612 Measured anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Subtracted 6079.19 6503.12 423.93
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Divided 6212.98 6655.12 1.07116
Ranked enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] 221.426 224.902 1.0157
pp1201 protein. [refseq;acc:nm_022152] Subtracted 217.446 214.2 3.246
Squared brain protein 16. [refseq;acc:nm_016458] Divided 26202.2 29043.8 1.10845
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Subtracted 23713.7 26223.8 2510.1
Rooted solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 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 Measured 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 6079.19 6503.12 423.93
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Divided 6035.6 6464.5 1.07106
Ranked 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] 182.378 185.241 1.0157
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 217.446 214.2 3.246
Squared ammecr1 protein. [refseq;acc:nm_015365] 23713.7 26223.8 2510.1
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Divided 15399.5 17067.9 1.10834
Rooted 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] 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 Measured nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 6035.6 6464.5 1.07106
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted 6079.19 6503.12 423.93
Ranked hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 213.897 1.0156
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 214.2 3.246
Squared mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] 23713.7 26223.8 2510.1
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Divided 15399.5 17067.9 1.10834
Rooted polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Subtracted 61.9703 64.1936 2.2233
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 54.1932 56.0802 1.03482
1615 Measured lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] 6035.6 6464.5 1.07106

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/