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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo 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
Hugo
description
Value Type
red
green
network_comparison
715 CPN1 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] Ranked 223.121 211.685 1.05402
EIF3M dendritic cell protein. [refseq;acc:nm_006360] Measured 6593.17 7364.55 1.117
MCFD2 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
716 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 61.0098
API5 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Squared 25911.5 30281.9 1.16867
CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Measured 6593.17 7364.55 1.117
CPZ cpz gene product. [refseq;acc:nm_003652] Ranked 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 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
HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Rooted 61.0111 65.3081 1.07043
SEC13 sec13-related protein. [swissprot;acc:p55735] Squared 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 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Ranked 223.121 211.685 1.05402
CPZ cpz gene product. [refseq;acc:nm_003652] Measured 6593.17 7364.55 1.117
FARSA 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
719 CPE 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
FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Rooted 60.7498 65.0218 1.07032
NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Ranked 247.769 235.074 1.054
SEC31A yeast sec31p homolog. [refseq;acc:nm_014933] Squared 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 jm1 protein. [refseq;acc:nm_014008] Rooted 61.5849 65.9155 1.07032
CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Measured 6593.17 7364.55 1.117
RPLP2 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Ranked 231.92 244.435 1.05396
721 ATP6V1E1 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
EXOC5 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Ranked 214.765 203.8 1.0538
PPIL4 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
STX7 syntaxin 7. [swissprot;acc:o15400] Measured 5580.97 6233.52 1.11692
722 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Rooted 58.4551 62.5601 1.07022
GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Squared 25911.7 30282.1 1.16867
HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Measured 8061.05 9002.33 1.11677
TREH 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 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 1.05274
DDX39 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
HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Measured 8056.09 8996.46 1.11673
POLR2E 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
724 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Ranked 244.842 232.577 1.05274
FARSA 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
GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Squared 25911.7 30282.1 1.16867
STX12 syntaxin 12. [refseq;acc:nm_177424] Rooted 61.3557 65.66 1.07015
725 ATP6V1D 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
FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Measured 5384.41 6012.82 1.11671
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Rooted 57.5045 53.7387 1.07008
MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Ranked 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 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Measured 6327.86 7064.13 1.11635
SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] Squared 25911.7 30282.1 1.16867
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Rooted 51.4482 55.0529 1.07006
727 ATP6V1H 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] Squared 25911.5 30281.9 1.16867
NUAK1 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Ranked 208.873 219.71 1.05188
RPL24 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Measured 7087.23 7911.25 1.11627

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/