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 1030 to 1079 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
515 tweety homolog 1; tweety homolog. [refseq;acc:nm_020659] Low confidence 205.156 198.715 1.03241
516 cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [swissprot;acc:q8wwm9]
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] High confidence 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
518 amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [swissprot;acc:q06481] Low confidence 205.156 198.715 1.03241
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] High confidence 250.858 234.563 1.06947
519 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 204.278 210.893 1.03238
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] High confidence 218.702 204.582 1.06902
520 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Low confidence 200.014 193.745 1.03236
sqv-7-like protein (fragment). [sptrembl;acc:o95454] High confidence 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
522 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 222.893 208.523
sam and sh3 domain containing 1. [refseq;acc:nm_015278] Low confidence 204.276 210.886 1.03236
523 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] High confidence 215.237 230.07 1.06891
ring finger protein 7; sensitive to apoptosis gene. [refseq;acc:nm_014245] Low confidence 203.162 196.796 1.03235
524 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] High confidence 215.237 230.07 1.06891
solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] 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
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 1.0323
526 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] High confidence 250.538 234.401 1.06884
solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0] Low confidence 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
528 solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168] 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
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
zinc finger protein 183-like 1. [refseq;acc:nm_178861] Low confidence 205.116 198.702 1.03228
530 solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [swissprot;acc:p11169] 205.541 199.114
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence 227.483 212.994 1.06803
531 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 223.356 209.149 1.06793
solute carrier family 2, facilitated glucose transporter, member 4 (glucose transporter type 4, insulin-responsive). [swissprot;acc:p14672] Low confidence 205.54 199.114 1.03227
532 glucose transporter 14. [refseq;acc:nm_153449] 205.541 199.115
zinc finger-like protein 9. [refseq;acc:nm_033414] High confidence 250.942 235.004 1.06782
533 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
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 1.03225
534 guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] High confidence 250.942 235.004 1.06782
zinc finger protein 216. [swissprot;acc:o76080] Low confidence 184.361 178.613 1.03218
535 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] High confidence 236.662 252.708 1.0678
protein associated with prk1. [refseq;acc:nm_019006] Low confidence 184.361 178.613 1.03218
536 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] High confidence 242.531 227.136 1.06778
ran binding protein 9; novel centrosomal protein ranbpm; ran binding protein, centrosomal. [refseq;acc:nm_005493] Low confidence 203.519 197.195 1.03207
537 megf11 protein. [refseq;acc:nm_032445] 207.951 201.517 1.03193
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] High confidence 229.803 215.301 1.06736
538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 237.627 253.604 1.06724
megf10 protein. [refseq;acc:nm_032446] Low confidence 207.949 201.517 1.03192
539 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] High confidence 236.964 252.86 1.06708
protein x 0001. [refseq;acc:nm_016302] Low confidence 199.661 193.489 1.0319
540 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] High confidence 222.156 208.201 1.06703

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/