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 2063 to 2112 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
516 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] Subtracted High confidence 248.463 234.095 14.368
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Divided 228.255 213.422 1.0695
517 forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [swissprot;acc:o43524] Low confidence 205.156 198.715 1.03241
metaxin 2. [swissprot;acc:o75431] High confidence 219.537 234.793 1.06949
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Subtracted Low confidence 203.167 196.732 6.435
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] High confidence 248.463 234.095 14.368
518 amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [swissprot;acc:q06481] Divided Low confidence 205.156 198.715 1.03241
megf11 protein. [refseq;acc:nm_032445] Subtracted 207.951 201.517 6.434
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Divided High confidence 250.858 234.563 1.06947
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 218.596 204.344 14.252
519 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Divided Low confidence 204.278 210.893 1.03238
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted High confidence 218.613 204.382 14.231
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 218.702 204.582 1.06902
solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] Subtracted Low confidence 205.551 199.117 6.434
520 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Divided 200.014 193.745 1.03236
megf10 protein. [refseq;acc:nm_032446] Subtracted 207.949 201.517 6.432
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] High confidence 223.356 209.149 14.207
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Divided 214.754 229.565 1.06897
521 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Low confidence 205.451 199.011 1.03236
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] High confidence 215.237 230.07 1.06891
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 218.702 204.582 14.12
solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [swissprot;acc:p22732] Low confidence 205.548 199.116 6.432
522 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Divided High confidence 222.893 208.523 1.06891
sam and sh3 domain containing 1. [refseq;acc:nm_015278] Low confidence 204.276 210.886 1.03236
solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0] Subtracted 205.549 199.117 6.432
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] High confidence 229.709 215.631 14.078
523 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Divided 215.237 230.07 1.06891
histone h2b.c (h2b/c). [swissprot;acc:q99880] Subtracted 247.47 233.441 14.029
ring finger protein 7; sensitive to apoptosis gene. [refseq;acc:nm_014245] Divided Low confidence 203.162 196.796 1.03235
solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168] Subtracted 205.543 199.115 6.428
524 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] 211.788 218.216
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Divided High confidence 215.237 230.07 1.06891
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Subtracted 247.47 233.441 14.029
solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] Divided Low confidence 205.551 199.117 1.03231
525 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] High confidence 215.237 230.07 1.06891
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 247.47 233.441 14.029
solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [swissprot;acc:p11169] Low confidence 205.541 199.114 6.427
solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [swissprot;acc:p22732] Divided 205.548 199.116 1.0323
526 histone h2b. [refseq;acc:nm_175055] Subtracted High confidence 247.47 233.441 14.029
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 250.538 234.401 1.06884
solute carrier family 2, facilitated glucose transporter, member 4 (glucose transporter type 4, insulin-responsive). [swissprot;acc:p14672] Subtracted Low confidence 205.54 199.114 6.426
solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0] Divided 205.549 199.117 1.0323
527 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] High confidence 248.56 232.579 1.06871
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Low confidence 208.004 201.497 1.03229
glucose transporter 14. [refseq;acc:nm_153449] Subtracted 205.541 199.115 6.426
histone h2b.s (h2b/s). [swissprot;acc:p57053] High confidence 247.47 233.441 14.029
528 histone h2b.d (h2b/d). [swissprot;acc:q99877]
solute carrier family 2, facilitated glucose transporter, member 1 (glucose transporter type 1, erythrocyte/brain) (hepg2 glucose transporter). [swissprot;acc:p11166] Low confidence 205.533 199.112 6.421
solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168] Divided 205.543 199.115 1.03228
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] High confidence 222.146 237.393 1.06864

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/