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 4758 to 4807 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
595 histone h2b. [refseq;acc:nm_175055] Measured Divided 3946.32 4475.47 1.13409
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Ranked Subtracted 207.26 194.346 12.914
vav proto-oncogene. [swissprot;acc:p15498] Divided 212.2 199.849 1.0618
596 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared 34129.6 40434.5 1.18473
cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted 60.0587 65.0057 1.08237
histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 4475.47 1.13409
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted Subtracted 54.4927 49.6125 4.8802
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured 4533.74 5279.4 745.66
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked 207.26 194.346 12.914
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Squared 31583.4 36221.8 4638.4
vav-3 protein. [swissprot;acc:q9ukw4] Ranked Divided 212.253 199.908 1.06175
597 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared 34129.4 40434.2 1.18473
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Rooted 60.0587 65.0057 1.08237
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured Subtracted 4533.74 5279.4 745.66
histone h2b.d (h2b/d). [swissprot;acc:q99877] Divided 3946.32 4475.47 1.13409
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted Subtracted 54.4927 49.6125 4.8802
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Ranked 207.26 194.346 12.914
vav-2 protein. [swissprot;acc:p52735] Divided 212.526 200.212 1.0615
vinculin (metavinculin). [swissprot;acc:p18206] Squared Subtracted 27463 32090.3 4627.3
598 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 34129.6 40434.5 1.18473
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured Subtracted 4533.74 5279.4 745.66
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 14728.8 19330.8 4602
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] Ranked 207.261 194.347 12.914
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Measured Divided 3946.32 4475.47 1.13409
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Rooted 61.2527 66.2644 1.08182
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Ranked 248.463 234.095 1.06138
thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted Subtracted 54.4927 49.6125 4.8802
599 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared Divided 34129.6 40434.5 1.18473
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] Rooted 138.375 127.926 1.08168
crk-like protein. [swissprot;acc:p46109] Ranked Subtracted 207.26 194.346 12.914
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Squared 28767.1 33317.5 4550.4
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Measured 4533.74 5279.4 745.66
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Ranked Divided 248.463 234.095 1.06138
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Rooted Subtracted 82.3879 87.2663 4.8784
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Measured Divided 3946.32 4475.47 1.13409
600 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Squared 34129.6 40434.5 1.18473
60s ribosomal protein l8. [swissprot;acc:p25120] Measured Subtracted 4533.74 5279.4 745.66
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Squared 28767.1 33317.5 4550.4
histone h2b.e (h2b/e). [swissprot;acc:q99879] Measured Divided 3946.32 4475.47 1.13409
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Ranked Subtracted 207.26 194.346 12.914
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Divided 248.463 234.095 1.06138
trs85 homolog. [swissprot;acc:q9y2l5] Rooted 138.375 127.926 1.08168
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 60.0742 64.9418 4.8676
601 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared Divided 34129.6 40434.5 1.18473
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Subtracted 28767.1 33317.5 4550.4
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Measured 4533.74 5279.4 745.66
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Ranked 207.26 194.346 12.914
step ii splicing factor slu7. [refseq;acc:nm_006425] Rooted 60.0742 64.9418 4.8676
symplekin. [swissprot;acc:q92797] Measured Divided 15213.4 13418.1 1.1338
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Ranked 206.274 218.792 1.06069

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/