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 63924 to 63973 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
4763 RAB23 Measured ras-related protein rab-23 (hspc137). [swissprot;acc:q9ulc3] Divided 8550.04 8659.33 1.01278
SMS Ranked spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] Subtracted 201.116 200.107 1.009
STXBP1 syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] Divided 200.018 199.036 1.00493
TRIP10 Squared cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 44782.1 44233 1.01241
Subtracted 549.1
4764 ANAPC1 Ranked anaphase-promoting complex 1 (meiotic checkpoint regulator). [refseq;acc:nm_022662] Divided 200.161 201.146 1.00492
APOA1BP Squared apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 47975.2 47388.3 1.01238
CDK8 Rooted cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Subtracted 70.3213 71.5004 1.1791
CTBP2 Measured c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 10232.6 10130.2 102.4
ELOVL4 Rooted elongation of very long chain fatty acids protein 4. [swissprot;acc:q9gzr5] Divided 70.3734 71.5529 1.01676
FZR1 Squared fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Subtracted 46042.5 46584 541.5
ITGB1BP3 Ranked muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 196.724 197.727 1.003
MRPS33 Measured mitochondrial 28s ribosomal protein s33 (s33mt) (mrp-s33) (cgi-139) (ptd003). [swissprot;acc:q9y291] Divided 8550.04 8659.33 1.01278
4765 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 7416.2 7518.37 102.17
ANAPC1 Ranked anaphase-promoting complex 1 (meiotic checkpoint regulator). [refseq;acc:nm_022662] 200.161 201.146 0.985
CDC2L6 Rooted cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076] 70.3218 71.5002 1.1784
LYST Measured lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] Divided 8232.92 8337.89 1.01275
MLH1 Squared dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 47993.1 47453.4 539.7
PDPK1 Ranked 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Divided 206.842 205.83 1.00492
PICK1 Rooted prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] 71.8821 73.0812 1.01668
RGS19 Squared regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 41196.2 40693.7 1.01235
4766 no value Measured gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] 8232.92 8337.89 1.01275
ATP6AP2 Squared vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787] Subtracted 50149.6 49610.8 538.8
IPO13 Measured importin 13; ran binding protein 13. [refseq;acc:nm_014652] 8127.17 8228.85 101.68
PCMT1 Ranked protein-l-isoaspartate(d-aspartate) o-methyltransferase (ec 2.1.1.77) (protein-beta-aspartate methyltransferase) (pimt) (protein l- isoaspartyl/d-aspartyl methyltransferase) (l-isoaspartyl protein carboxyl methyltransferase). [swissprot;acc:p22061] Divided 206.842 205.83 1.00492
PHC3 Rooted polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 73.0124 74.2254 1.01661
RGS20 Squared regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] 41196.2 40693.7 1.01235
SAMSN1 Rooted sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Subtracted 72.6624 71.4875 1.1749
STXBP1 Ranked syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] 200.018 199.036 0.982
4767 CHEK1 Squared serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] 50149.6 49610.8 538.8
CTRL Measured proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] 7877.1 7977.78 100.68
MLL5 myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, drosophila). [refseq;acc:nm_182931] Divided 7836.97 7936.3 1.01267
PIGS Ranked gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52] 198.971 197.998 1.00491
Subtracted 0.973
RGS17 Squared regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided 41196.2 40693.7 1.01235
RPL19 Rooted 60s ribosomal protein l19. [swissprot;acc:p14118] 69.3079 70.4555 1.01656
SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Subtracted 72.6632 71.4895 1.1737
4768 BOK Squared bcl2-related ovarian killer. [refseq;acc:nm_032515] 27306.3 26768.5 537.8
CSRP3 Rooted lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided 69.2825 70.4241 1.01648
GNAO1 Squared guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 41196.2 40693.7 1.01235
MRPL3 Rooted mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Subtracted 69.2175 70.391 1.1735
PITRM1 Ranked metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 188.213 187.295 1.0049
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted 203.126 202.155 0.971
VPS4A Measured vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245] 7772.88 7873.48 100.6
YLPM1 nuclear protein zap3 (zap113). [swissprot;acc:p49750] Divided 8167.12 8270.02 1.0126
4769 ATG3 Ranked apg3p; pc3-96 protein. [refseq;acc:nm_022488] 177.446 176.597 1.00481
EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Subtracted 202.127 201.193 0.934
GYS2 Measured glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 8857 8967.97 1.01253
PRAM1 Rooted pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 71.2585 72.4297 1.1712
SAMSN1 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Divided 72.6624 71.4875 1.01644

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/