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 3063 to 3112 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
766 TRIOBP Ranked protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 213.804 224.226 1.04875
TST Rooted thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 63.5181 67.7402 1.06647
767 no value Ranked rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
ATP5O Squared atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 24509.4 28571.6 1.16574
MPST Rooted 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 63.5181 67.7402 1.06647
UGP2 Measured utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 6691.21 7444.22 1.11254
768 DNAJB4 Ranked dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 1.04873
EIF5 Squared eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 12108.4 14114.6 1.16569
RHOA Rooted transforming protein rhoa (h12). [swissprot;acc:p06749] 63.5181 67.7402 1.06647
UBE2V2 Measured ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] 6690.44 7443.29 1.11253
769 no value Rooted 60s ribosomal protein l39. [swissprot;acc:p02404] 55.6817 59.3786 1.06639
ATP6V1F Measured vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] 5873.77 6532.44 1.11214
NAGS Squared n-acetylglutamate synthase. [refseq;acc:nm_153006] 20943 24412.8 1.16568
PERLD1 Ranked cab2. [refseq;acc:nm_033419] 210.946 221.225 1.04873
770 no value Measured 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] 5874.74 6533.34 1.11211
Rooted 60s ribosomal protein l18a. [swissprot;acc:q02543] 55.6817 59.3786 1.06639
DNAJB5 Ranked dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 210.946 221.225 1.04873
FBLN2 Squared fibulin-2 precursor. [swissprot;acc:p98095] 45189.6 52666.2 1.16545
771 API5 Measured apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 5874.74 6533.34 1.11211
DNAJB1 Ranked dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] 210.946 221.225 1.04873
QRSL1 Squared glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 24418 28453.7 1.16528
RPS19 Rooted 40s ribosomal protein s19. [swissprot;acc:p39019] 55.6817 59.3786 1.06639
772 ETF1 Ranked eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 210.946 221.225 1.04873
FAAH Squared fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 24418 28453.7 1.16528
RPL31 Rooted 60s ribosomal protein l31. [swissprot;acc:p12947] 55.6817 59.3786 1.06639
SEC13 Measured sec13-related protein. [swissprot;acc:p55735] 5874.76 6533.36 1.11211
773 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] 5874.74 6533.34
COTL1 Squared coactosin-like protein. [swissprot;acc:q14019] 24418 28453.7 1.16528
PPP1CC Rooted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 127.967 120.003 1.06637
VPS52 Ranked suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] 210.946 221.225 1.04873
774 DPM1 Rooted dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 65.3248 69.648 1.06618
MCFD2 Ranked multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
SEC31A Measured yeast sec31p homolog. [refseq;acc:nm_014933] 5874.76 6533.36 1.11211
UNG Squared uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 24418 28453.7 1.16528
775 no value Ranked histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541 1.04854
ATP6V1G1 Measured 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] 5874.74 6533.33 1.11211
CLTC Rooted clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 62.2385 58.38 1.06609
PET112L Squared probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 24418 28453.7 1.16528
776 no value Ranked dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 225.996 215.535 1.04854
Rooted sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 59.6869 63.6262 1.066
GDAP1L1 Measured ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 5874.76 6533.36 1.11211
RPS13 Squared 40s ribosomal protein s13. [swissprot;acc:q02546] 21976 25607.9 1.16527
777 DDX39 Measured dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 5874.74 6533.34 1.11211
HDAC1 Ranked histone deacetylase 1 (hd1). [swissprot;acc:q13547] 225.989 215.53 1.04853
KPNA3 Squared importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 33908.1 39510.9 1.16523
SPRY3 Rooted sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 59.6869 63.6262 1.066
778 ATP6V1B1 Measured 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] 5874.63 6533.23 1.11211
MAD2L1 Squared mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 32174 37487.2 1.16514
SNX6 Ranked sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
SPRY1 Rooted sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 59.6869 63.6262 1.066

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/