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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1513 to 1562 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
48 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Measured Subtracted Low confidence 0 5240.94 4840.17 400.77
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked Divided High confidence 1 65.4586 83.0461 1.26868
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted Low confidence 0 13825.5 17020.5 3195
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared Divided High confidence 960.518 176.164 5.45241
importin 9. [refseq;acc:nm_018085] Rooted Subtracted 21.8651 29.828 7.9629
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared Divided 1 6300.2 10703.5 1.69891
latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302] Rooted Subtracted Low confidence 0 16.1864 10.5357 5.6507
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 1 137.446 120.823 16.623
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared Low confidence 82347.8 61881.5 20466.3
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted Divided 0 9.84765 5.80678 1.69589
mstp028 protein. [refseq;acc:nm_031954] Squared Subtracted 105962 110835 4873
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Ranked Divided High confidence 9830 6909 1.42278
pnas-129. [sptrembl;acc:q9bxv8] Measured Low confidence 366.666 151.073 2.42708
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared Subtracted High confidence 1 210199 136638 73561
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted Divided Low confidence 66.6504 75.3798 1.13097
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Ranked 242.742 217.217 1.11751
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] Subtracted High confidence 0 18359.8 14447.8 3912
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted Divided 1 27.7254 44.0299 1.58807
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Squared Low confidence 0 14.8569 83.2781 5.60535
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked Subtracted High confidence 1 350 290 60
transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Measured Divided Low confidence 8313.02 9645.34 1.16027
trophinin. [swissprot;acc:q12816] Squared 82347.8 61881.5 1.33073
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured Subtracted High confidence 24806.9 20369.9 4437
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Rooted Divided 0 15.0533 9.31487 1.61605
49 60s ribosomal protein l18a. [swissprot;acc:q02543] Squared Subtracted Low confidence 21978 26833.6 4855.6
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] High confidence 11625.2 6483.52 5141.68
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 1 28994.2 17134.8 1.69212
bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Ranked Low confidence 0 14607.1 11141.9 1.31101
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 1 133 105 1.26667
brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 1.41927
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Measured Subtracted 1 24806.9 20369.9 4437
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 131906 69990
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Low confidence 48.8531 56.7071 7.854
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked High confidence 350 290 60
dead-box protein. [refseq;acc:nm_018665] 0 10628.3 14486 3857.7
dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Rooted Low confidence 14.7386 9.094 5.6446
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Squared Divided High confidence 8.10857 43.7473 5.39519
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Measured Subtracted 153 662 509
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted Divided Low confidence 1 66.6623 75.3751 1.1307
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Measured Subtracted 0 2988.27 2589.09 399.18
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared Divided 1 122475 159767 1.30449
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted High confidence 27.7254 44.0299 1.58807
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 137.446 120.823 16.623
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared Low confidence 82347.8 61881.5 20466.3
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 0 13825.5 17020.5 3195
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured Divided 1 13470.1 11654.4 1.1558
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 0 266 645 2.42481
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 1 779.167 1390.33 1.78438
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Rooted Low confidence 0 16.9115 0.00001 1691150
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Subtracted High confidence 21.8651 29.828 7.9629

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/