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.


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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3050 to 3099 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
763 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Squared 21186.4 24698.3 1.16576
N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Ranked 228.78 218.091 1.04901
PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Measured 4250.54 4729.67 1.11272
764 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Squared 21186.4 24698.3 1.16576
CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Rooted 63.5181 67.7402 1.06647
PFKL 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Measured 4250.18 4729.12 1.11269
PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Ranked 222.082 211.707 1.04901
765 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
POLS polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Measured 4726.38 5258.95 1.11268
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Rooted 63.5181 67.7402 1.06647
SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Squared 21186.4 24698.3 1.16576
766 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 24509.4 28571.6 1.16574
TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Measured 6691.93 7445.09 1.11255
TRIOBP protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Ranked 213.804 224.226 1.04875
TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Rooted 63.5181 67.7402 1.06647
767 no value rho interacting protein 3. [refseq;acc:nm_015134] Ranked 213.803 224.224 1.04874
ATP5O atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Squared 24509.4 28571.6 1.16574
MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Rooted 63.5181 67.7402 1.06647
UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Measured 6691.21 7444.22 1.11254
768 DNAJB4 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Ranked 210.946 221.225 1.04873
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Squared 12108.4 14114.6 1.16569
RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] Rooted 63.5181 67.7402 1.06647
UBE2V2 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] Measured 6690.44 7443.29 1.11253
769 no value 60s ribosomal protein l39. [swissprot;acc:p02404] Rooted 55.6817 59.3786 1.06639
ATP6V1F 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] Measured 5873.77 6532.44 1.11214
NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] Squared 20943 24412.8 1.16568
PERLD1 cab2. [refseq;acc:nm_033419] Ranked 210.946 221.225 1.04873
770 no value 60s ribosomal protein l18a. [swissprot;acc:q02543] Rooted 55.6817 59.3786 1.06639
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] Measured 5874.74 6533.34 1.11211
DNAJB5 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Ranked 210.946 221.225 1.04873
FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Squared 45189.6 52666.2 1.16545
771 API5 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Measured 5874.74 6533.34 1.11211
DNAJB1 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] Ranked 210.946 221.225 1.04873
QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Squared 24418 28453.7 1.16528
RPS19 40s ribosomal protein s19. [swissprot;acc:p39019] Rooted 55.6817 59.3786 1.06639
772 ETF1 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Ranked 210.946 221.225 1.04873
FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Squared 24418 28453.7 1.16528
RPL31 60s ribosomal protein l31. [swissprot;acc:p12947] Rooted 55.6817 59.3786 1.06639
SEC13 sec13-related protein. [swissprot;acc:p55735] Measured 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 coactosin-like protein. [swissprot;acc:q14019] Squared 24418 28453.7 1.16528
PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Rooted 127.967 120.003 1.06637
VPS52 suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Ranked 210.946 221.225 1.04873
774 DPM1 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] Rooted 65.3248 69.648 1.06618
MCFD2 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Ranked 225.996 215.535 1.04854
SEC31A yeast sec31p homolog. [refseq;acc:nm_014933] Measured 5874.76 6533.36 1.11211
UNG uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Squared 24418 28453.7 1.16528
775 no value histone deacetylase 2 (hd2). [swissprot;acc:q92769] Ranked 226.003 215.541 1.04854
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] Measured 5874.74 6533.33 1.11211
CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Rooted 62.2385 58.38 1.06609

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/