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 2180 to 2229 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
273 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Divided 3199.4 3870.8 1.20985
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Squared 16120.1 20665.7 1.28198
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 74.1074 1.12103
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Measured Subtracted 5181.2 6410.58 1229.38
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted 57.45 66.332 8.882
274 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Squared 30807.7 39351.7 8544
60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 242.744 266.07 23.326
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Measured Divided 3119.98 2579.49 1.20953
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Rooted Subtracted 57.4586 66.3336 8.875
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Divided 66.1063 74.1068 1.12102
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 241.373 267.352 1.10763
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 16120.1 20665.7 1.28198
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Measured Subtracted 5181.2 6410.58 1229.38
275 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 23.283
adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 8.8112
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided 66.1048 74.0977 1.12091
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked 241.373 267.352 1.10763
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Measured Subtracted 10264.9 9043.51 1221.39
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared Divided 16120.1 20665.7 1.28198
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 3119.98 2579.49 1.20953
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Squared Subtracted 59331.2 67833.7 8502.5
276 60s ribosomal protein l32. [swissprot;acc:p02433] Ranked Divided 241.13 266.969 1.10716
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 258.437 235.183 23.254
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted 128.909 120.173 8.736
gbp protein isoform a. [refseq;acc:nm_017870] Measured 699.76 1894.39 1194.63
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted Divided 66.1046 74.0964 1.1209
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Squared 16120.1 20665.7 1.28198
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Measured 3119.98 2579.49 1.20953
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared Subtracted 33100.3 41520.6 8420.3
277 40s ribosomal protein s29. [swissprot;acc:p30054] Ranked Divided 241.849 267.642 1.10665
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 239.277 262.434 23.157
cerebral cell adhesion molecule. [refseq;acc:nm_016174] Squared 62198.5 70599.4 8400.9
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Measured 8600.02 9792.49 1192.47
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Divided 3119.98 2579.49 1.20953
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Rooted 65.9938 73.9449 1.12048
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 104.459 113.143 8.684
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Squared Divided 16120.1 20665.7 1.28198
278 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked 241.399 267.088 1.10642
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Squared 16120.1 20665.7 1.28198
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted 34018.3 42373 8354.7
myelin gene expression factor 2. [refseq;acc:nm_016132] Ranked 235.383 258.476 23.093
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Measured 8600.02 9792.49 1192.47
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Rooted Divided 65.9938 73.9449 1.12048
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Subtracted 57.3527 65.7973 8.4446
transcription factor lbx1. [swissprot;acc:p52954] Measured Divided 3119.98 2579.49 1.20953
279 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared Subtracted 30596.2 38919.9 8323.7
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted 42.0574 50.4237 8.3663
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Ranked Divided 252.644 228.42 1.10605
mosaic protein lgn. [swissprot;acc:p81274] Measured 3119.98 2579.49 1.20953
musashi 2 isoform a. [refseq;acc:nm_138962] Squared 15569.5 19953.6 1.28158

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/