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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 3408 to 3457 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
852 ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Squared 31100.1 36086.4 1.16033
853 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Measured 4078.45 4502.32 1.10393
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Squared 31100.1 36086.4 1.16033
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Rooted 64.0287 68.0566 1.06291
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Ranked 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Rooted 64.0316 68.0597 1.06291
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Squared 31100.2 36086.5 1.16033
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured 6562.98 7242.37 1.10352
855 ero1-like. [refseq;acc:nm_014584]
espin. [refseq;acc:nm_031475] Squared 31100.1 36086.4 1.16033
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Rooted 64.0262 68.0537 1.0629
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Ranked 178.514 171.42 1.04138
856 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Squared 31100.1 36086.4 1.16033
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Measured 5210.58 5749.33 1.1034
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Rooted 58.5944 62.2766 1.06284
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked 215.028 206.623 1.04068
857 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Rooted 58.6002 62.2793 1.06278
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Measured 5210.58 5749.33 1.1034
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Squared 31100.1 36086.4 1.16033
putatative 28 kda protein. [refseq;acc:nm_020143] Ranked 227.241 236.467 1.0406
858 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Rooted 65.1843 69.2736 1.06273
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]

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/