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.


Navigation/Query Panel:
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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2882 to 2931 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
721 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
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
728 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Measured 6000.23 6696.89 1.11611
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] Ranked 208.874 219.708 1.05187
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Rooted 59.7414 63.909 1.06976
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] Squared 25911.8 30282.2 1.16866
729 exocyst complex component sec15a. [swissprot;acc:q8tag9] Rooted 62.5069 66.8603 1.06965
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Ranked 208.874 219.708 1.05187
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] Measured 6000.23 6696.89 1.11611
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Squared 25910.8 30280.9 1.16866
730 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Measured 6000.23 6696.89 1.11611
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Squared 24644.9 28800.7 1.16863
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Rooted 62.5729 66.9286 1.06961
mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Ranked 208.874 219.708 1.05187
731 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Rooted 98.2298 91.8648 1.06929
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Ranked 208.874 219.708 1.05187
methyltransferase like 2. [refseq;acc:nm_018396] Measured 13241.4 11864 1.1161
vinculin (metavinculin). [swissprot;acc:p18206] Squared 27463 32090.3 1.16849
732 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 13241.4 11864 1.1161
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Rooted 51.8444 48.4963 1.06904
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Ranked 124.434 118.318 1.05169
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Squared 26029.8 30414.4 1.16845
733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Ranked 164 155.961 1.05154
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured 13241.4 11864 1.1161
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Rooted 52.0099 55.5904 1.06884

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/