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 5058 to 5107 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2529 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Subtracted 201.96 201.488 0.472
2530 chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] 187.902 188.366 0.464
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Divided 212.464 211.99 1.00224
2531 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 216.264 215.787 1.00221
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Subtracted 215.964 216.421 0.457
2532 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
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Subtracted 217.144 216.699 0.445
2533 paraspeckle protein 1. [refseq;acc:nm_018282] Divided 190.417 190.824 1.00214
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Subtracted 217.144 216.699 0.445
2534 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 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
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Subtracted 224.726 225.164 0.438
2536 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] Divided 236.51 236.008 1.00213
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Subtracted 218.068 217.633 0.435
2537 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 212.67 212.262 0.408
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Divided 215.964 216.421 1.00212
2538 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
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 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 217.144 216.699 1.00205
paraspeckle protein 1. [refseq;acc:nm_018282] Subtracted 190.417 190.824 0.407
2540 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
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Divided 217.144 216.699 1.00205
2541 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 194.505 194.902 1.00204
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
2542 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 217.587 217.988 0.401
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Divided 218.068 217.633 1.002
2543 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
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Divided 224.726 225.164 1.00195
2544 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 212.67 212.262 1.00192
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Subtracted 194.505 194.902 0.397
2545 elongation factor 2 (ef-2). [swissprot;acc:p13639] 222.658 223.047 0.389
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
2546 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Subtracted 222.658 223.047 0.389
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 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 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Divided 217.587 217.988 1.00184
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Subtracted 206.902 206.519 0.383
2551 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Divided 209.766 210.148 1.00182
Subtracted 0.382
2552 s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 212.953 212.572 0.381
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Divided 193.12 193.467 1.0018
2553 44050 protein. [refseq;acc:nm_178832] Subtracted 151.386 151.009 0.377
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 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

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/