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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1732 to 1781 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
network_comparison
green
433 PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 1.15091 6036.38
434 SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Squared 18306.1 1.21438 22230.6
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 54.4927 1.09837 49.6125
TBX6 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 1.07934 229.411
UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 1.15077 6037.37
435 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 1.21372 32283.5
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 1.07909 205.286
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 1.1507 6022.6
RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 50.832 1.09769 46.3081
436 CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 1.21372 32283.5
PXN paxillin. [swissprot;acc:p49023] Ranked 221.522 1.07909 205.286
SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 6230.94 1.15042 7168.2
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted 210.928 1.09764 192.165
437 CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 1.21372 32283.5
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured 3779.92 1.15042 4348.48
TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Ranked 209.921 1.07878 226.459
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Rooted 51.0466 1.09751 56.024
438 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Ranked 233.723 1.07869 216.674
ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Measured 6252.58 1.15039 7192.88
BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Rooted 55.1867 1.09722 60.5522
SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Squared 28863.2 1.21371 35031.5
439 no value dok-like protein. [refseq;acc:nm_024872] Rooted 63.2134 1.09711 69.352
CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Squared 51616.7 1.21198 42588.9
PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Measured 6252.58 1.15039 7192.88
RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Ranked 238.986 1.07866 257.784
440 no value dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Squared 26348.4 1.21168 31925.8
CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Measured 6251.91 1.15038 7192.08
DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Rooted 63.2134 1.09711 69.352
NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 1.07843 249.983
441 DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Rooted 63.2134 1.09711 69.352
GCA grancalcin. [swissprot;acc:p28676] Measured 6251.96 1.15038 7192.13
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 1.07835 207.222
TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Squared 26348.7 1.21161 31924.3
442 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Ranked 223.802 1.0783 207.55
CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared 51286.6 1.21146 42334.5
FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Rooted 63.2134 1.09711 69.352
SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Measured 6251.99 1.15038 7192.17
443 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Rooted 50.1766 1.09707 45.7369
ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Measured 6252.27 1.15038 7192.51
MTIF2 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Squared 26472.8 1.21135 32067.7
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Ranked 223.79 1.0783 207.539
444 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted 50.1636 1.09701 45.7275
EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Measured 3758.67 1.15011 4322.87
NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Ranked 223.801 1.0783 207.549
UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 58831 1.21091 48584.2
445 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked 223.801 1.0783 207.549
NOC3L ad24 protein. [refseq;acc:nm_022451] Measured 3753.71 1.14978 4315.95
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Rooted 50.1635 1.09701 45.7274
UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared 58831 1.21091 48584.2
446 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Rooted 54.9019 1.0967 60.2111

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/