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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2863 to 2912 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
716 CPXM2 Measured potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 6593.17 7364.55 1.117
CPZ Ranked cpz gene product. [refseq;acc:nm_003652] 223.121 211.685 1.05402
717 CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
CPN1 Measured carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 6593.17 7364.55 1.117
HDAC1 Rooted histone deacetylase 1 (hd1). [swissprot;acc:q13547] 61.0111 65.3081 1.07043
SEC13 Squared sec13-related protein. [swissprot;acc:p55735] 25911.7 30282.1 1.16867
718 ATP6V1G3 vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] 25911.5 30281.9
CPXM1 Ranked potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 223.121 211.685 1.05402
CPZ Measured cpz gene product. [refseq;acc:nm_003652] 6593.17 7364.55 1.117
FARSA Rooted phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 60.7498 65.0218 1.07032
719 CPE Measured carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 6593.17 7364.55 1.117
FARS2 Rooted phenylalanine-trna synthetase. [refseq;acc:nm_006567] 60.7498 65.0218 1.07032
NOL5A Ranked nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 247.769 235.074 1.054
SEC31A Squared yeast sec31p homolog. [refseq;acc:nm_014933] 25911.7 30282.1 1.16867
720 ATP6V1G1 vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] 25911.5 30281.9
CCDC22 Rooted jm1 protein. [refseq;acc:nm_014008] 61.5849 65.9155 1.07032
CPXM1 Measured potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 6593.17 7364.55 1.117
RPLP2 Ranked 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 231.92 244.435 1.05396
721 ATP6V1E1 Squared vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] 25911.7 30282.1 1.16867
EXOC5 Ranked exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 214.765 203.8 1.0538
PPIL4 Rooted peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 60.8463 65.123 1.07029
STX7 Measured syntaxin 7. [swissprot;acc:o15400] 5580.97 6233.52 1.11692
722 DYNC1I1 Rooted dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 58.4551 62.5601 1.07022
GDAP1L1 Squared ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 25911.7 30282.1 1.16867
HARS2 Measured histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 8061.05 9002.33 1.11677
TREH Ranked trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] 217.952 206.902 1.05341
723 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 1.05274
DDX39 Squared dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 25911.5 30281.9 1.16867
HARS Measured histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 8056.09 8996.46 1.11673
POLR2E Rooted dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 51.7007 48.3103 1.07018
724 no value Ranked dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 244.842 232.577 1.05274
FARSA Measured phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 5384.41 6012.82 1.11671
GDAP1 Squared ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 25911.7 30282.1 1.16867
STX12 Rooted syntaxin 12. [refseq;acc:nm_177424] 61.3557 65.66 1.07015
725 ATP6V1D Squared vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] 25911.7 30282.1 1.16867
FARS2 Measured phenylalanine-trna synthetase. [refseq;acc:nm_006567] 5384.41 6012.82 1.11671
HNRPM Rooted heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 57.5045 53.7387 1.07008
MVK Ranked mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 235.296 247.673 1.0526
726 FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 244.495 232.419 1.05196
MLH3 Measured dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 6327.86 7064.13 1.11635
SEC31B Squared secretory pathway component sec31b-1. [refseq;acc:nm_015490] 25911.7 30282.1 1.16867
TBL3 Rooted transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 51.4482 55.0529 1.07006
727 ATP6V1H Squared vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] 25911.5 30281.9 1.16867
NUAK1 Ranked probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] 208.873 219.71 1.05188
RPL24 Measured 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 7087.23 7911.25 1.11627
SF3A3 Rooted splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 59.7414 63.909 1.06976
728 ASNSD1 Measured hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 6000.23 6696.89 1.11611
ATP6V1B2 Squared vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 25911.8 30282.2 1.16866
B3GNT1 Ranked n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] 208.874 219.708 1.05187
SF3A1 Rooted splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] 59.7414 63.909 1.06976

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
- Hugo is the HGNC identifier if it exists
- 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/