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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5062 to 5111 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
2531 VPS45 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Subtracted 215.964 216.421 0.457
2532 C21orf66 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 217.144 216.699 0.445
NONO 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Divided 190.405 190.812 1.00214
2533 PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] 190.417 190.824
TLR2 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Subtracted 217.144 216.699 0.445
2534 GPD2 glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Divided 208 207.555 1.00214
Subtracted 0.445
2535 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] 224.726 225.164 0.438
CBX1 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] Divided 188.228 188.63 1.00214
2536 GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 236.51 236.008 1.00213
ING4 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Subtracted 218.068 217.633 0.435
2537 AMT aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 212.67 212.262 0.408
VPS45 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Divided 215.964 216.421 1.00212
2538 NONO 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Subtracted 190.405 190.812 0.407
SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Divided 190.765 191.163 1.00209
2539 C21orf66 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 217.144 216.699 1.00205
PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Subtracted 190.417 190.824 0.407
2540 no value proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 213.494 213.088 0.406
TLR2 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Divided 217.144 216.699 1.00205
2541 CBX1 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] Subtracted 188.228 188.63 0.402
DARS aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Divided 194.505 194.902 1.00204
2542 EPN2 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Subtracted 217.587 217.988 0.401
ING4 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Divided 218.068 217.633 1.002
2543 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] 224.726 225.164 1.00195
SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Subtracted 190.765 191.163 0.398
2544 AMT aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Divided 212.67 212.262 1.00192
DARS aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Subtracted 194.505 194.902 0.397
2545 no value proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Divided 213.494 213.088 1.00191
EEF2 elongation factor 2 (ef-2). [swissprot;acc:p13639] Subtracted 222.658 223.047 0.389
2546 GRM2 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]
TAF9B tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Divided 197.138 197.507 1.00187
2547 no value glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 206.894 206.51 1.00186
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 222.658 223.047 0.389
2548 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Divided 206.899 206.516 1.00185
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Subtracted 206.894 206.51 0.384
2549 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Divided 206.902 206.519 1.00185
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Subtracted 206.899 206.516 0.383
2550 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 206.902 206.519
EPN2 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Divided 217.587 217.988 1.00184
2551 FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 209.766 210.148 1.00182
Subtracted 0.382
2552 CDY1B testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Divided 193.12 193.467 1.0018
MAT2A s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Subtracted 212.953 212.572 0.381
2553 C10orf83 44050 protein. [refseq;acc:nm_178832] 151.386 151.009 0.377
CDYL chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Divided 193.12 193.467 1.0018
2554 CDY2B testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]
PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Subtracted 151.386 151.009 0.377
2555 MAT2A s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Divided 212.953 212.572 1.00179
TAF9B tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Subtracted 197.138 197.507 0.369
2556 AURKB serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] 219.907 220.267 0.36

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/