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 25176 to 25225 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2645 probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Ranked Divided 194.097 194.328 1.00119
2646 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Measured Subtracted 8936.97 8999.55 62.58
gbp protein isoform a. [refseq;acc:nm_017870] Squared 1182.25 1726.55 544.3
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Rooted Divided 60.4039 60.7697 1.00606
Subtracted 0.3658
mct-1 protein. [refseq;acc:nm_014060] Measured Divided 4778.28 4732.13 1.00975
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Squared 35558.6 36579.1 1.0287
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Ranked Subtracted 187.075 186.84 0.235
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided 213.169 213.417 1.00116
2647 adiponectin receptor 2. [refseq;acc:nm_024551] Squared Subtracted 13573.9 14111.2 537.3
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Ranked 216.934 216.7 0.234
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Measured 4508.81 4446.41 62.4
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Squared Divided 35558.6 36579.1 1.0287
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Rooted 60.4039 60.7697 1.00606
Subtracted 0.3658
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Measured Divided 4778.28 4732.13 1.00975
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Ranked 212.496 212.25 1.00116
2648 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Rooted Subtracted 61.19 60.8333 0.3567
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Squared 22249 22757.3 508.3
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] Ranked 216.933 216.7 0.233
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Squared Divided 35558.6 36579.1 1.0287
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Ranked 213.169 213.417 1.00116
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Rooted 80.1033 79.6263 1.00599
tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Measured 6365.03 6424.56 1.00935
Subtracted 59.53
2649 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Rooted Divided 61.19 60.8333 1.00586
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Subtracted 56.7402 57.0913 0.3511
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared 22249 22757.3 508.3
jm4 protein. [refseq;acc:nm_007213] Measured Divided 7133.06 7067.09 1.00933
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Ranked 213.63 213.874 1.00114
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] Subtracted 216.933 216.7 0.233
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Squared Divided 35558.6 36579.1 1.0287
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Measured Subtracted 5935.71 5876.22 59.49
2650 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Squared Divided 16658.1 16197 1.02847
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Measured 9150.44 9234.09 1.00914
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Rooted 57.8738 58.2094 1.0058
kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685] Ranked 217.188 216.942 1.00113
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Measured Subtracted 5935.71 5876.22 59.49
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Squared 22249 22757.3 508.3
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Ranked 216.937 216.704 0.233
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Rooted 52.8957 53.243 0.3473
2651 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Measured Divided 9150.44 9234.09 1.00914
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] Ranked Subtracted 217.176 216.944 0.232
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Squared 22249 22757.3 508.3
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Rooted Divided 70.0476 70.4321 1.00549
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Ranked 201.37 201.594 1.00111
tumor protein d52 (n8 protein). [swissprot;acc:p55327] Measured Subtracted 6349.55 6407.25 57.7
ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670] Squared Divided 34028.7 33090.4 1.02836
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted Subtracted 52.8957 53.243 0.3473
2652 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Squared 22249 22757.3 508.3

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/