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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 844 to 893 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
red
green
network_comparison
422 RGN Subtracted senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 238.704 255.68 16.976
423 OPHN1 oligophrenin 1. [swissprot;acc:o60890]
RAB26 Divided ras-related protein rab-26. [swissprot;acc:q9ulw5] 240.287 260.193 1.08284
424 GTPBP4 Subtracted nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 251.83 234.951 16.879
POLR2C Divided dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 240.287 260.193 1.08284
425 ENDOG Subtracted endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 16.864
MAX Divided max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
426 AIFM1 Subtracted programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 212.547 229.411 16.864
DCTN5 Divided dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 1.08197
427 POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 259.525 1.08146
TBX6 Subtracted t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 212.547 229.411 16.864
428 DDX54 Divided atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 234.808 1.0811
LSM5 Subtracted u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 16.86
429 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514 16.83
POLR3G Divided polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 1.08064
430 LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 1.07995
PPAN-P2RY11 Subtracted suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 250.938 234.134 16.804
431 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 16.792
TRUB1 Divided trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 255.113 1.07987
432 ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
MCTS1 Subtracted mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 16.717
433 AIFM1 Divided programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 212.547 229.411 1.07934
MRPL22 Subtracted mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 16.717
434 NOC3L ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 16.662
TBX6 Divided t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 212.547 229.411 1.07934
435 POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 205.286 1.07909
WDR12 Subtracted wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 251.299 234.729 16.57
436 PXN Divided paxillin. [swissprot;acc:p49023] 221.522 205.286 1.07909
TPI1 Subtracted triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 231.496 248.048 16.552
437 TRIP10 Divided cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 226.459 1.07878
Subtracted 16.538
438 ARD1A Divided n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 216.674 1.07869
BOP1 Subtracted block of proliferation 1. [swissprot;acc:q14137] 250.794 234.433 16.361
439 PES1 pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 16.356
RPS9 Divided 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
440 no value Subtracted 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 16.354
NDC80 Divided highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 249.983 1.07843
441 GRAP grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 207.222 1.07835
TIMM22 Subtracted mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225 226.578 16.353
442 ANKS1B Divided e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
ATPAF2 Subtracted atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 210.225 226.578 16.353
443 NAV2 Divided neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 223.79 207.539 1.0783
UQCRB Subtracted ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 210.225 226.578 16.353
444 NAV1 Divided neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549 1.0783
NOL1 Subtracted proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 250.053 233.725 16.328
445 GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 250.858 234.563 16.295
NAV3 Divided neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 223.801 207.549 1.0783
446 GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 224.049 207.785 1.07827
Subtracted 16.264
447 NEK2 Divided serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 1.07827

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
- Hugo is the HGNC identifier if it exists
- 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/