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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Gene Rank description Value Type Network Comparison Type green Interaction Map Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 1518 to 1567 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
green
Filtered
red
network_comparison
380 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Divided 15138.2 1 12998.5 1.16461
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 1833.64 0 1927.62 1.05125
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Subtracted 5588.75 1 4641.09 947.66
381 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Divided 2633.79 0 2509.05 1.04972
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Subtracted 600 559.333 40.667
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Divided 6109.31 1 5246.01 1.16456
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 5588.75 4641.09 947.66
382 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 359.98 0 377.445 1.04852
lamin b2. [swissprot;acc:q03252] Subtracted 538.704 579.262 40.558
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Divided 5279.4 1 4533.74 1.16447
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted 3343.62 2397.19 946.43
383 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 87.5499 0 47.4756 40.0743
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 362.023 379.489 1.04825
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 5279.4 1 4533.74 1.16447
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 5192.61 4247.36 945.25
384 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 739.623 0 703.068 36.555
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Divided 5279.4 1 4533.74 1.16447
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Subtracted 9002.33 8061.05 941.28
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Divided 8627.63 0 8243.06 1.04665
385 40s ribosomal protein s28. [swissprot;acc:p25112] 405.367 387.486 1.04615
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Subtracted 8996.46 1 8056.09 940.37
kappa b-ras 1. [refseq;acc:nm_020345] 1117.36 0 1153.15 35.79
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Divided 5279.4 1 4533.74 1.16447
386 60s ribosomal protein l8. [swissprot;acc:p25120]
dok-like protein. [refseq;acc:nm_024872] Subtracted 0 0 35 35
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 892.67 1 1833.01 940.34
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 2254.12 0 2156.64 1.0452
387 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1330.37 1388.29 1.04354
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted 892.67 1 1833.01 940.34
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Divided 5279.4 4533.74 1.16447
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Subtracted 2668.56 0 2633.61 34.95
388 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1161.29 1195.87 34.58
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Divided 5279.4 1 4533.74 1.16447
scratch; scratch 1. [refseq;acc:nm_031309] 1339.9 0 1398.21 1.04352
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Subtracted 7192.88 1 6252.58 940.3
389 enigma protein; lim domain protein. [refseq;acc:nm_005451] 153 0 187.25 34.25
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Divided 12011.7 11512.3 1.04338
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 5279.4 1 4533.74 1.16447
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Subtracted 7192.88 6252.58 940.3
390 alpha crystallin a chain. [swissprot;acc:p02489] 89.2447 0 55.3059 33.9388
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 7192.51 1 6252.27 940.24
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Divided 12011.7 0 11512.3 1.04338
rw1 protein (fragment). [swissprot;acc:q92545] 5279.4 1 4533.74 1.16447
391 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 2371.24 0 2403.53 32.29
seven in absentia homolog 1. [refseq;acc:nm_003031] Divided 2316.94 2221.04 1.04318
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Subtracted 7192.17 1 6251.99 940.18
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided 3144.39 3658.76 1.16358
392 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 219.891 0 229.211 1.04238
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 4236.95 1 3641.89 1.16339
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Subtracted 7192.08 6251.91 940.17

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/