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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Value Type Gene Rank Interaction Map description Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
251 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Subtracted 0 270.264 142.417 127.847
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1 4579.34 5940.64 1361.3
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Divided 0 1225.08 1079.38 1.13498
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 1 6417.18 7859.6 1.22477
252 crk-like protein. [swissprot;acc:p46109]
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Subtracted 0 2039.47 2164.92 125.45
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 1 9648.27 10994.9 1346.63
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Divided 0 1225.08 1079.38 1.13498
253 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Subtracted 1 9642.22 10986.4 1344.18
espin. [refseq;acc:nm_031475] Divided 0 1225.07 1079.38 1.13498
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Subtracted 556 681 125
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 1 6417.18 7859.59 1.22477
254 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 1318.22 1495.66 1.13461
dc11 protein. [refseq;acc:nm_020186] Subtracted 556 681 125
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 1 9634.98 10976.2 1341.22
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 6417.18 7859.6 1.22477
255 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 0 1317.84 1495.22 1.1346
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Subtracted 2509.05 2633.79 124.74
mad protein (max dimerizer). [swissprot;acc:q05195] 1 4455.95 5774.03 1318.08
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 6417.18 7859.6 1.22477
256 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 6417.19 7859.51 1.22476
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Subtracted 0 3967.18 4091.59 124.41
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Divided 1224.65 1079.77 1.13418
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Subtracted 1 4456.67 5773.77 1317.1
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided 6417.31 7858.12 1.22452
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 0 861.401 759.896 1.13358
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Subtracted 488.43 612.604 124.174
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1 4456.93 5773.67 1316.74
258 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 0 1183.16 1337.54 1.13048
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Subtracted 130.512 6.50325 124.009
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 1 6417.33 7857.93 1.22449
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 4457.06 5773.63 1316.57
259 60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 0 1295.49 1463.51 1.1297
myosin vi. [swissprot;acc:q9um54] Subtracted 345.865 224.096 121.769
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 1 6417.81 7852.52 1.22355
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 4569.48 5885.79 1316.31
260 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 0 1388.45 1268.19 120.26
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1 12515.4 11221.1 1294.3
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 4244.95 5193.42 1.22343
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 0 1949.36 2202 1.1296
261 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1295.81 1463.55 1.12945
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Subtracted 205.439 86.9525 118.486
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 1 4247.36 5192.61 1.22255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 4571.89 5864.86 1292.97
262 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Divided 0 764.479 676.971 1.12926
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 1 24896.4 20431.7 1.21852
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Subtracted 0 606.049 723.75 117.701
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1 4571.89 5864.86 1292.97
263 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 0 498.07 615.233 117.163
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 1 4571.89 5864.86 1292.97

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/