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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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 2901 to 2950 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
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
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Squared 26029.1 30413.6 1.16845
734 loh1cr12. [refseq;acc:nm_058169] Rooted 57.805 61.7803 1.06877
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Ranked 232.601 244.534 1.0513
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Measured 13241.4 11864 1.1161
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Squared 26032.5 30417.7 1.16845
735 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 26030.5 30415.2 1.16844
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Ranked 232.601 244.534 1.0513
unr protein. [swissprot;acc:o75534] Rooted 57.805 61.7803 1.06877
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Measured 5768.32 6434.78 1.11554
736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Ranked 232.601 244.534 1.0513
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared 22017.1 25721.9 1.16827
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Measured 5768.32 6434.78 1.11554
wd-repeat protein 3. [swissprot;acc:q9unx4] Rooted 51.5438 55.0853 1.06871
737 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Measured 5768.32 6434.78 1.11554
pnas-18. [sptrembl;acc:q9bzu3] Rooted 97.8205 91.5467 1.06853
septin 10 isoform 1. [refseq;acc:nm_144710] Ranked 125.526 119.402 1.05129
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Squared 31479.4 36770.8 1.16809
738 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Measured 5768.32 6434.78 1.11554
syntaxin 7. [swissprot;acc:o15400] Rooted 61.5022 65.7076 1.06838

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/