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 2858 to 2907 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
715 dendritic cell protein. [refseq;acc:nm_006360] Measured 6593.17 7364.55 1.117
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Rooted 61.0097 65.3071 1.07044
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared 25911.5 30281.9 1.16867
716 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
cpz gene product. [refseq;acc:nm_003652] Ranked 223.121 211.685 1.05402
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Rooted 61.0098 65.3071 1.07044
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Measured 6593.17 7364.55 1.117
717 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Ranked 223.121 211.685 1.05402
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] Measured 6593.17 7364.55 1.117
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Rooted 61.0111 65.3081 1.07043
sec13-related protein. [swissprot;acc:p55735] Squared 25911.7 30282.1 1.16867
718 cpz gene product. [refseq;acc:nm_003652] Measured 6593.17 7364.55 1.117
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Rooted 60.7498 65.0218 1.07032
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Ranked 223.121 211.685 1.05402
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] Squared 25911.5 30281.9 1.16867
719 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Measured 6593.17 7364.55 1.117
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Ranked 247.769 235.074 1.054
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Rooted 60.7498 65.0218 1.07032
yeast sec31p homolog. [refseq;acc:nm_014933] Squared 25911.7 30282.1 1.16867
720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Ranked 231.92 244.435 1.05396
jm1 protein. [refseq;acc:nm_014008] Rooted 61.5849 65.9155 1.07032
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Measured 6593.17 7364.55 1.117
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] Squared 25911.5 30281.9 1.16867
721 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Ranked 214.765 203.8 1.0538
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Rooted 60.8463 65.123 1.07029
syntaxin 7. [swissprot;acc:o15400] Measured 5580.97 6233.52 1.11692
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] Squared 25911.7 30282.1 1.16867
722 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Rooted 58.4551 62.5601 1.07022
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Squared 25911.7 30282.1 1.16867
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Measured 8061.05 9002.33 1.11677
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Ranked 217.952 206.902 1.05341
723 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Squared 25911.5 30281.9 1.16867
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Rooted 51.7007 48.3103 1.07018
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Measured 8056.09 8996.46 1.11673
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Ranked 244.842 232.577 1.05274
724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Squared 25911.7 30282.1 1.16867
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Measured 5384.41 6012.82 1.11671
syntaxin 12. [refseq;acc:nm_177424] Rooted 61.3557 65.66 1.07015
725 heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 57.5045 53.7387 1.07008
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Ranked 235.296 247.673 1.0526
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Measured 5384.41 6012.82 1.11671
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] Squared 25911.7 30282.1 1.16867
726 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Measured 6327.86 7064.13 1.11635
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Ranked 244.495 232.419 1.05196
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Squared 25911.7 30282.1 1.16867
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Rooted 51.4482 55.0529 1.07006
727 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Measured 7087.23 7911.25 1.11627
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Ranked 208.873 219.71 1.05188
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Rooted 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
- 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/