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.


Navigation/Query Panel:
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 6858 to 6907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
858 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Squared Subtracted 23148.8 27021.5 3872.7
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Measured 6393.81 6984.94 591.13
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Squared Divided 31100.1 36086.4 1.16033
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Measured 5210.58 5749.33 1.1034
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Rooted Subtracted 62.2361 58.3858 3.8503
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Ranked 221.306 212.806 8.5
syntaxin 12. [refseq;acc:nm_177424] Divided 217.446 208.997 1.04043
859 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 1.04031
d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Squared 31100.1 36086.4 1.16033
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Subtracted 25044.9 28915.2 3870.3
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Measured Divided 5210.58 5749.33 1.1034
nostrin. [refseq;acc:nm_052946] Subtracted 4682.87 4093.05 589.82
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked 50.7983 42.3003 8.498
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Rooted 62.2361 58.3858 3.8503
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Divided 53.3429 50.2017 1.06257
860 60s ribosomal protein l18a. [swissprot;acc:q02543] Ranked 234.025 224.958 1.04031
eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured Subtracted 4682.87 4093.05 589.82
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Squared 25043.9 28914 3870.1
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Divided 24242.8 28127.6 1.16025
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Ranked Subtracted 242.024 233.544 8.48
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Rooted 62.2361 58.3858 3.8503
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Measured Divided 5210.58 5749.33 1.1034
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Rooted 60.6929 64.4864 1.0625
861 40s ribosomal protein s19. [swissprot;acc:p39019] Ranked 234.025 224.958 1.04031
apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Rooted 51.8245 55.0559 1.06235
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Measured 5734.15 6326.41 1.10329
dna repair protein rad52 homolog. [swissprot;acc:p43351] Rooted Subtracted 62.2361 58.3858 3.8503
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 25043.4 28913.4 3870
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured 4682.87 4093.05 589.82
ring finger protein 44. [refseq;acc:nm_014901] Squared Divided 24242.8 28127.6 1.16025
syntaxin 12. [refseq;acc:nm_177424] Ranked Subtracted 217.446 208.997 8.449
862 60s ribosomal protein l31. [swissprot;acc:p12947] Divided 234.025 224.958 1.04031
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Rooted 76.0455 80.7777 1.06223
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Measured Subtracted 4682.87 4093.05 589.82
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Squared Divided 24242.8 28127.6 1.16025
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Measured 4076.72 4497.74 1.10327
prohibitin. [swissprot;acc:p35232] Rooted Subtracted 63.4547 67.3003 3.8456
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Ranked 231.357 239.778 8.421
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Squared 24999.1 28856.8 3857.7
863 40s ribosomal protein s30. [swissprot;acc:q05472] 28134.5 31984.1 3849.6
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Ranked Divided 240.194 230.957 1.03999
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Measured Subtracted 4682.87 4093.05 589.82
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Rooted Divided 62.7551 66.6474 1.06202
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Measured 5595.65 6173.23 1.10322
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Rooted Subtracted 63.4547 67.3003 3.8456
ring finger protein 38. [refseq;acc:nm_022781] Squared Divided 24242.8 28127.6 1.16025
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked Subtracted 215.028 206.623 8.405
864 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Squared 22245.5 26087.5 3842
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Ranked Divided 240.194 230.957 1.03999
exocyst complex component sec8. [swissprot;acc:q96a65] Subtracted 217.762 209.449 8.313

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/