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 3480 to 3529 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
435 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Squared Subtracted 30408.3 36092.8 5684.5
436 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured Divided 6230.94 7168.2 1.15042
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 32283.5 1.21372
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Measured Subtracted 6739.83 7644.63 904.8
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Rooted 66.082 71.6525 5.5705
paxillin. [swissprot;acc:p49023] Ranked Divided 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
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Squared Subtracted 28990.9 34656.4 5665.5
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Ranked 231.496 248.048 16.552
437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Divided 209.921 226.459 1.07878
Subtracted 16.538
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Measured 6739.83 7644.63 904.8
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Rooted 66.082 71.6525 5.5705
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared Divided 26598.9 32283.5 1.21372
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Subtracted 28980.7 34643.6 5662.9
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured Divided 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
block of proliferation 1. [swissprot;acc:q14137] Ranked Subtracted 250.794 234.433 16.361
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Rooted 66.082 71.6525 5.5705
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Squared 28967 34626.4 5659.4
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Ranked Divided 233.723 216.674 1.07869
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Measured Subtracted 6739.85 7644.63 904.78
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Divided 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
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 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

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/