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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 812 to 861 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
406 Subtracted NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 17.558 237.109 254.667
407 Divided MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 1.08673 239.75 260.544
Subtracted NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 17.558 237.109 254.667
408 Divided CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 1.08649 255.112 234.804
Subtracted HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 17.558 237.109 254.667
409 Divided POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 1.08641 241.045 261.874
Subtracted RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 17.558 237.109 254.667
410 Divided no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 1.0864 233.376 253.539
Subtracted HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 17.558 237.109 254.667
411 Divided GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 1.0864 233.376 253.539
Subtracted RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] 17.558 237.109 254.667
412 Divided UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 1.08567 240.788 261.416
Subtracted NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 17.379 251.926 234.547
413 Divided POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 1.08525 240.913 261.45
Subtracted TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 17.302 223.202 205.9
414 Divided KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 1.08522 232.431 252.238
Subtracted MAX max protein. [swissprot;acc:p25912] 17.267 227.828 210.561
415 Divided KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 1.08514 232.382 252.166
Subtracted TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 17.163 200.586 183.423
416 Divided POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 1.08496 240.6 261.041
Subtracted TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] 17.131 200.791 183.66
417 Divided SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 1.08417 233.539 253.197
Subtracted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 17.103 235.94 218.837
418 Divided CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 1.08417 233.539 253.197
Subtracted ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 17.049 233.723 216.674
419 Divided FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 1.08417 233.539 253.197
Subtracted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16.997 235.922 218.925
420 Divided CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 1.08417 233.539 253.197
Subtracted CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 16.976 238.704 255.68
421 Divided TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 1.08403 223.202 205.9
Subtracted ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 16.976 238.704 255.68
422 Divided RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] 1.08284 240.287 260.193
Subtracted RGN senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 16.976 238.704 255.68
423 Divided RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] 1.08284 240.287 260.193
Subtracted OPHN1 oligophrenin 1. [swissprot;acc:o60890] 16.976 238.704 255.68
424 Divided POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 1.08284 240.287 260.193
Subtracted GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 16.879 251.83 234.951
425 Divided MAX max protein. [swissprot;acc:p25912] 1.082 227.828 210.561
Subtracted ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 16.864 212.547 229.411
426 Divided DCTN5 dynactin 4. [refseq;acc:nm_032486] 1.08197 233.142 252.253
Subtracted AIFM1 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 16.864 212.547 229.411
427 Divided POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 1.08146 239.977 259.525
Subtracted TBX6 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 16.864 212.547 229.411
428 Divided DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 1.0811 253.852 234.808
Subtracted LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 16.86 227.748 210.888
429 Divided POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 1.08064 239.709 259.038
Subtracted EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 16.83 251.344 234.514
430 Divided LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 1.07995 227.748 210.888
Subtracted PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 16.804 250.938 234.134
431 Divided TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 1.07987 236.245 255.113

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/