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 3430 to 3479 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
858 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Squared 31100.1 36086.4 1.16033
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Measured 5210.58 5749.33 1.1034
syntaxin 12. [refseq;acc:nm_177424] Ranked 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
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 5210.58 5749.33 1.1034
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Rooted 53.3429 50.2017 1.06257
860 60s ribosomal protein l18a. [swissprot;acc:q02543] Ranked 234.025 224.958 1.04031
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Squared 24242.8 28127.6 1.16025
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Measured 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
ring finger protein 44. [refseq;acc:nm_014901] Squared 24242.8 28127.6 1.16025
862 60s ribosomal protein l31. [swissprot;acc:p12947] Ranked 234.025 224.958 1.04031
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Rooted 76.0455 80.7777 1.06223
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Squared 24242.8 28127.6 1.16025
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Measured 4076.72 4497.74 1.10327
863 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Ranked 240.194 230.957 1.03999
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Rooted 62.7551 66.6474 1.06202
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Measured 5595.65 6173.23 1.10322
ring finger protein 38. [refseq;acc:nm_022781] Squared 24242.8 28127.6 1.16025
864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Ranked 240.194 230.957 1.03999
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Squared 24242.8 28127.6 1.16025
ring finger protein 44. [refseq;acc:nm_014901] Measured 5595.65 6173.23 1.10322
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Rooted 62.7551 66.6474 1.06202
865 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Measured 5595.65 6173.23 1.10322
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Squared 24242.8 28127.6 1.16025
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Ranked 211.961 203.814 1.03997
866 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Squared 24242.8 28127.6 1.16025
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Rooted 51.8306 55.0247 1.06163
ring finger protein 38. [refseq;acc:nm_022781] Measured 5595.65 6173.23 1.10322
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Ranked 221.306 212.806 1.03994
867 40s ribosomal protein s3a. [swissprot;acc:p49241] 225.689 234.674 1.03981
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Rooted 61.668 65.4526 1.06137
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Squared 24242.8 28127.6 1.16025
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Measured 5595.65 6173.23 1.10322
868 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Ranked 233.298 242.571 1.03975
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Squared 31099.4 36082.4 1.16023
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Rooted 61.668 65.4526 1.06137
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Measured 5595.65 6173.23 1.10322
869 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
exocyst complex component sec8. [swissprot;acc:q96a65] Ranked 217.762 209.449 1.03969
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Rooted 61.668 65.4526 1.06137
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Squared 20273.1 23521.2 1.16022
870 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Rooted 84.6378 89.8201 1.06123
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Measured 5595.65 6173.23 1.10322
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Squared 21086.3 24464.1 1.16019

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/