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 [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
network_comparison
green
1608 UBC ubiquitin. [swissprot;acc:p02248] Measured Divided 6158.22 1.07134 6597.55
1609 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Ranked Subtracted 207.916 3.254 204.662
DCLK1 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Measured 6297.05 424.03 6721.08
EIF2S3 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Squared 24291.6 2510.8 26802.4
PSMB5 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 1.03494 67.884
PSMD10 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Measured 5826.74 1.07134 6242.44
SALL4 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Rooted Subtracted 61.9701 2.2234 64.1935
UGP2 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 1.0158 204.876
WTAP wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Squared 28992.5 1.10876 32145.6
1610 EIF5A2 eif-5a2 protein. [refseq;acc:nm_020390] Measured 6222.4 1.07126 6665.83
FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted 6079.19 423.93 6503.12
KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Squared Divided 15639.2 1.10866 17338.5
RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Ranked Subtracted 217.446 3.246 214.2
SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Rooted Divided 67.4766 1.03489 69.831
SNAP91 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 61.9701 2.2234 64.1935
TMF1 tata element modulatory factor (tmf). [swissprot;acc:p82094] Squared 23713.7 2510.1 26223.8
UBE2V2 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 1.01579 204.886
1611 no value heat shock factor binding protein 1. [swissprot;acc:o75506] Squared 27263.5 1.10865 30225.7
CEP70 p10-binding protein. [refseq;acc:nm_024491] Ranked 221.313 1.01577 217.877
MOCS2 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Measured Subtracted 6079.19 423.93 6503.12
PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Rooted Divided 67.4958 1.03486 69.8487
RERE arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Subtracted 61.9705 2.2233 64.1938
SCYL1 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 23713.7 2510.1 26223.8
TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Ranked 217.446 3.246 214.2
TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Measured Divided 5497.73 1.07119 5132.35
1612 no value brain protein 16. [refseq;acc:nm_016458] Squared 26202.2 1.10845 29043.8
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Ranked 221.426 1.0157 224.902
ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Measured Subtracted 6079.19 423.93 6503.12
EIF5AP1 eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Divided 6212.98 1.07116 6655.12
NUP98 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Squared Subtracted 23713.7 2510.1 26223.8
SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Rooted Divided 67.5045 1.03485 69.8568
TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Ranked Subtracted 217.446 3.246 214.2
USP8 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Rooted 61.9703 2.2233 64.1936
1613 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365] Squared 23713.7 2510.1 26223.8
FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Ranked 217.446 3.246 214.2
HTATIP2 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] Divided 182.378 1.0157 185.241
MRPS22 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Measured 6035.6 1.07106 6464.5
NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Squared 15399.5 1.10834 17067.9
ROD1 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 2.2233 64.1936
RPL29 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Measured 6079.19 423.93 6503.12
SLC5A6 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Rooted Divided 67.511 1.03484 69.8628
1614 no value nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Measured 6035.6 1.07106 6464.5
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked Subtracted 217.446 3.246 214.2
FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Measured 6079.19 423.93 6503.12
FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Ranked Divided 217.233 1.0156 213.897
NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Squared 15399.5 1.10834 17067.9
PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted 54.1932 1.03482 56.0802
PTBP2 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Subtracted 61.9703 2.2233 64.1936
RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Squared 23713.7 2510.1 26223.8
1615 AAK1 adaptor-associated kinase 1. [refseq;acc:nm_014911] Rooted 61.9703 2.2233 64.1936

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
- Hugo is the HGNC identifier if it exists
- 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/