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 3508 to 3557 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
439 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Rooted Subtracted 66.082 71.6525 5.5705
pescadillo homolog 1. [swissprot;acc:o00541] Ranked 251.297 234.941 16.356
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Measured Divided 6252.58 7192.88 1.15039
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 6739.85 7644.63 904.78
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Squared 28937.1 34588.8 5651.7
440 40s ribosomal protein s26. [swissprot;acc:p02383] Ranked 210.224 226.578 16.354
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Measured Divided 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
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Subtracted 66.082 71.6525 5.5705
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked Divided 231.802 249.983 1.07843
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured Subtracted 6740.5 7644.76 904.26
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Squared 27096.7 32743.5 5646.8
441 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 25860 31475.4 5615.4
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Divided 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
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Subtracted 66.082 71.6525 5.5705
grancalcin. [swissprot;acc:p28676] Measured Divided 6251.96 7192.13 1.15038
grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 207.222 1.07835
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Subtracted 210.225 226.578 16.353
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 902.27
442 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Ranked 210.225 226.578 16.353
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared Divided 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
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Squared Subtracted 33908.1 39510.9 5602.8
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Rooted 66.082 71.6523 5.5703
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured 5189 6088.47 899.47
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Divided 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
calcyphosine. [swissprot;acc:q13938] Subtracted 5189 6088.47 899.47
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 Divided 223.79 207.539 1.0783
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Rooted Subtracted 66.082 71.6523 5.5703
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Squared 33900.6 39498 5597.4
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Divided 26472.8 32067.7 1.21135
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Ranked Subtracted 210.225 226.578 16.353
444 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted Divided 50.1636 45.7275 1.09701
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured Subtracted 5189 6088.47 899.47
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Rooted 87.2414 92.8092 5.5678
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Ranked Divided 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
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Ranked Subtracted 250.053 233.725 16.328
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Squared 26472.8 32067.7 5594.9
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 58831 48584.2 1.21091
445 ad24 protein. [refseq;acc:nm_022451] Measured 3753.71 4315.95 1.14978
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Subtracted 1857.32 958.237 899.083
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Rooted 66.0829 71.6462 5.5633
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Squared 33893.6 39486.1 5592.5
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked Divided 223.801 207.549 1.0783

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/