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 1180 to 1229 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
590 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 217.215 204.279 1.06333
591 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Subtracted 217.67 230.596 12.926
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Divided 216.72 230.439 1.0633
592 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Subtracted 217.67 230.596 12.926
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 91.63 97.4011 1.06298
593 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Subtracted 217.67 230.596 12.926
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided 232.118 218.406 1.06278
594 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 207.26 194.346 12.914
595 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
vav proto-oncogene. [swissprot;acc:p15498] Divided 212.2 199.849 1.0618
596 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Subtracted 207.26 194.346 12.914
vav-3 protein. [swissprot;acc:q9ukw4] Divided 212.253 199.908 1.06175
597 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 207.26 194.346 12.914
vav-2 protein. [swissprot;acc:p52735] Divided 212.526 200.212 1.0615
598 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] Subtracted 207.261 194.347 12.914
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 248.463 234.095 1.06138
599 crk-like protein. [swissprot;acc:p46109] Subtracted 207.26 194.346 12.914
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] Divided 248.463 234.095 1.06138
600 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 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
601 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Subtracted 207.26 194.346 12.914
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Divided 206.274 218.792 1.06069
602 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Subtracted 207.26 194.346 12.914
603 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 12.902
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Divided 225.829 212.945 1.0605
604 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Subtracted 207.272 194.371 12.901
605 histone h2b.c (h2b/c). [swissprot;acc:q99880] Divided 247.47 233.441 1.0601
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Subtracted 225.829 212.945 12.884
606 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Divided 247.47 233.441 1.0601
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Subtracted 207.309 194.452 12.857
607 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Divided 247.47 233.441 1.0601
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Subtracted 216.731 229.549 12.818
608 dynein light chain 2. [refseq;acc:nm_080677]
histone h2b. [refseq;acc:nm_175055] Divided 247.47 233.441 1.0601
609 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Subtracted 226.523 213.786 12.737
histone h2b.s (h2b/s). [swissprot;acc:p57053] Divided 247.47 233.441 1.0601
610 histone h2b.d (h2b/d). [swissprot;acc:q99877]
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Subtracted 205.74 193.021 12.719
611 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Divided 247.47 233.441 1.0601
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 228.986 216.276 12.71
612 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 205.89 193.183 12.707
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Divided 247.47 233.441 1.0601
613 histone h2b.e (h2b/e). [swissprot;acc:q99879]
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Subtracted 247.769 235.074 12.695
614 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Divided 214.257 202.125 1.06002
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Subtracted 232.468 245.048 12.58
615 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 241.907 229.35 12.557

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/