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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7862 to 7911 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
983 tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Measured Subtracted 5350.87 5896.82 545.95
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked 211.987 204.964 7.023
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Measured Divided 6654.42 7296.51 1.09649
984 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Subtracted 5568.96 6113.35 544.39
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted Divided 56.1854 53.2272 1.05558
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Subtracted 56.781 60.2344 3.4534
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Measured Divided 6362.64 6976.1 1.09642
ns1-associated protein 1. [refseq;acc:nm_006372] Squared Subtracted 15043.7 18560.1 3516.4
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Ranked 211.987 204.964 7.023
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 116.71 120.654 1.03379
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Squared 59338.5 68268.3 1.15049
985 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Rooted Subtracted 62.4582 65.9096 3.4514
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 4264.46 544.28
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared 15043.7 18560.1 3516.4
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Measured Divided 6362.64 6976.1 1.09642
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Squared 22569.9 25956.6 1.15005
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Ranked 233.402 225.782 1.03375
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Subtracted 211.987 204.964 7.023
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Rooted Divided 61.9502 65.389 1.05551
986 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Measured Subtracted 6436.19 6980.13 543.94
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Rooted Divided 62.4582 65.9096 1.05526
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared Subtracted 15053 18568 3515
exocyst complex component sec5. [swissprot;acc:q96kp1] Ranked Divided 116.771 120.707 1.03371
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Measured 6362.64 6976.1 1.09642
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Squared 22569.9 25956.6 1.15005
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Rooted Subtracted 62.4582 65.9096 3.4514
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Ranked 211.987 204.964 7.023
987 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] Rooted 62.4582 65.9096 3.4514
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Squared 21186.4 24698.3 3511.9
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Measured Divided 6660.04 7301.81 1.09636
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Squared 20465.9 23535.3 1.14998
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Ranked Subtracted 211.987 204.964 7.023
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 218.459 211.338 1.03369
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Measured Subtracted 5511.2 6054.71 543.51
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Rooted Divided 62.4582 65.9096 1.05526
988 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Squared 18082.5 20792.7 1.14988
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Measured Subtracted 6618.74 7161.67 542.93
katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 54.4988 51.0573 3.4415
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Ranked Divided 218.461 211.343 1.03368
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 236.679 243.679 7
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Measured Divided 6229.69 6829.58 1.0963
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Squared Subtracted 21186.4 24698.3 3511.9
989 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Rooted Divided 67.7394 71.4737 1.05513
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Subtracted 54.1916 57.6307 3.4391
kccr13l. [refseq;acc:nm_139179] Squared Divided 23339.9 26834.1 1.14971
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Measured Subtracted 5707.73 6249.1 541.37
pp1201 protein. [refseq;acc:nm_022152] Squared 21186.4 24698.3 3511.9
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Ranked Divided 218.462 211.345 1.03367
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Measured 11743.3 10712.3 1.09624

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/