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 1730 to 1779 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
433 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 1.09837
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 6036.38 1.15091
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 212.547 229.411 1.07934
434 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 22230.6 1.21438
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 54.4927 49.6125 1.09837
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
435 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 50.832 46.3081 1.09769
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 32283.5 1.21372
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 205.286 1.07909
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507
436 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 7168.2 1.15042
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 32283.5 1.21372
paxillin. [swissprot;acc:p49023] Ranked 221.522 205.286 1.07909
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted 210.928 192.165 1.09764
437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Ranked 209.921 226.459 1.07878
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 32283.5 1.21372
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured 3779.92 4348.48 1.15042
zinc finger protein t86. [swissprot;acc:o00488] Rooted 51.0466 56.024 1.09751
438 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Squared 28863.2 35031.5 1.21371
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 60.5522 1.09722
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Ranked 233.723 216.674 1.07869
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 7192.88 1.15039
439 40s ribosomal protein s9. [swissprot;acc:p46781] Ranked 238.986 257.784 1.07866
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Squared 51616.7 42588.9 1.21198
dok-like protein. [refseq;acc:nm_024872] Rooted 63.2134 69.352 1.09711
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Measured 6252.58 7192.88 1.15039
440 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 6251.91 7192.08 1.15038
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Squared 26348.4 31925.8 1.21168
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Rooted 63.2134 69.352 1.09711
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 249.983 1.07843
441 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Squared 26348.7 31924.3 1.21161
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Rooted 63.2134 69.352 1.09711
grancalcin. [swissprot;acc:p28676] Measured 6251.96 7192.13 1.15038
grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 207.222 1.07835
442 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared 51286.6 42334.5 1.21146
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Ranked 223.802 207.55 1.0783
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Measured 6251.99 7192.17 1.15038
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Rooted 63.2134 69.352 1.09711
443 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 50.1766 45.7369 1.09707
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Measured 6252.27 7192.51 1.15038
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 223.79 207.539 1.0783
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Squared 26472.8 32067.7 1.21135
444 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted 50.1636 45.7275 1.09701
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Ranked 223.801 207.549 1.0783
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Measured 3758.67 4322.87 1.15011
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 58831 48584.2 1.21091
445 ad24 protein. [refseq;acc:nm_022451] Measured 3753.71 4315.95 1.14978
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked 223.801 207.549 1.0783
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Rooted 50.1635 45.7274 1.09701

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/