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 Value Type description 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
Value Type
description
red
green
network_comparison
852 Rooted peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 58.5869 62.2732 1.06292
853 Measured apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 4078.45 4502.32 1.10393
Ranked wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 108.289 112.772 1.0414
Squared ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] 31100.1 36086.4 1.16033
Rooted target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 64.0287 68.0566 1.06291
854 Measured uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 6562.98 7242.37 1.10352
Ranked cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 108.289 112.772 1.0414
Squared keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 31100.2 36086.5 1.16033
Rooted importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 64.0316 68.0597 1.06291
855 Measured ero1-like. [refseq;acc:nm_014584] 6562.98 7242.37 1.10352
Ranked tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 178.514 171.42 1.04138
Squared espin. [refseq;acc:nm_031475] 31100.1 36086.4 1.16033
Rooted importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 64.0262 68.0537 1.0629
856 Measured heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] 5210.58 5749.33 1.1034
Ranked xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] 215.028 206.623 1.04068
Squared cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 31100.1 36086.4 1.16033
Rooted mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] 58.5944 62.2766 1.06284
857 Measured n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] 5210.58 5749.33 1.1034
Ranked putatative 28 kda protein. [refseq;acc:nm_020143] 227.241 236.467 1.0406
Squared pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 31100.1 36086.4 1.16033
Rooted mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] 58.6002 62.2793 1.06278
858 Measured n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] 5210.58 5749.33 1.1034
Ranked syntaxin 12. [refseq;acc:nm_177424] 217.446 208.997 1.04043
Squared lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] 31100.1 36086.4 1.16033
Rooted 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] 65.1843 69.2736 1.06273
859 Measured 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] 5210.58 5749.33 1.1034
Ranked 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 1.04031
Squared d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] 31100.1 36086.4 1.16033
Rooted trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 53.3429 50.2017 1.06257
860 Measured protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] 5210.58 5749.33 1.1034
Ranked 60s ribosomal protein l18a. [swissprot;acc:q02543] 234.025 224.958 1.04031
Squared neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] 24242.8 28127.6 1.16025
Rooted werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 60.6929 64.4864 1.0625
861 Measured bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 5734.15 6326.41 1.10329
Ranked 40s ribosomal protein s19. [swissprot;acc:p39019] 234.025 224.958 1.04031
Squared ring finger protein 44. [refseq;acc:nm_014901] 24242.8 28127.6 1.16025
Rooted apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 51.8245 55.0559 1.06235
862 Measured probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 4076.72 4497.74 1.10327
Ranked 60s ribosomal protein l31. [swissprot;acc:p12947] 234.025 224.958 1.04031
Squared phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 24242.8 28127.6 1.16025
Rooted adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 76.0455 80.7777 1.06223
863 Measured neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] 5595.65 6173.23 1.10322
Ranked casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 240.194 230.957 1.03999
Squared ring finger protein 38. [refseq;acc:nm_022781] 24242.8 28127.6 1.16025
Rooted hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 62.7551 66.6474 1.06202
864 Measured ring finger protein 44. [refseq;acc:nm_014901] 5595.65 6173.23 1.10322
Ranked casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 240.194 230.957 1.03999
Squared phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] 24242.8 28127.6 1.16025
Rooted 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] 62.7551 66.6474 1.06202
865 Measured phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 5595.65 6173.23 1.10322

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/