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 5541 to 5590 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
693 EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Rooted Divided 51.3598 55.1508 1.07381
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Subtracted 3199.4 3870.8 671.4
NOVA1 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Ranked Divided 222.554 234.847 1.05524
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Measured 7725.1 8647.74 1.11943
694 CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Ranked Subtracted 217.602 206.195 11.407
CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Squared Divided 33104 38818.5 1.17262
EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Rooted Subtracted 50.0578 54.5502 4.4924
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Measured Divided 7725.1 8647.74 1.11943
KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared Subtracted 23517.1 27867.3 4350.2
NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Measured 6075.55 6746.92 671.37
POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Ranked Divided 241.907 229.35 1.05475
PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Rooted 68.4526 73.4852 1.07352
695 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 50.0578 54.5502 4.4924
ACOX2 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Squared 27382 31722.9 4340.9
ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Measured 5768.32 6434.78 666.46
HIVEP1 zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Divided 7725.1 8647.74 1.11943
KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Rooted 63.17 67.8116 1.07348
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked Subtracted 210.739 199.398 11.341
PPIL4 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Divided 226.135 214.405 1.05471
SGPL1 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Squared 22778.5 26693.1 1.17186
696 no value 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
methyltransferase like 2. [refseq;acc:nm_018396] Rooted Subtracted 100.169 95.6772 4.4918
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Measured Divided 7725.1 8647.74 1.11943
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Squared Subtracted 19568.3 23904.6 4336.3
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Ranked 210.739 199.398 11.341
PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Rooted Divided 68.433 73.4502 1.07332
SFRS18 sr rich protein. [refseq;acc:nm_032870] Ranked 225.293 213.64 1.05455
SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Measured Subtracted 5768.32 6434.78 666.46
697 ACBD3 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]
CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Squared 19556 23891.8 4335.8
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Rooted 100.169 95.6772 4.4918
FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Ranked Divided 220.444 209.113 1.05419
Subtracted 11.331
KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Rooted Divided 63.1944 67.8162 1.07314
OAT ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Squared 22778.5 26693.1 1.17186
SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Measured 7105.27 7953.71 1.11941
698 ACP1 red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Squared 17850.2 20913.9 1.17163
ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Measured 7101.95 7949.85 1.11939
BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Squared Subtracted 19546.1 23881.6 4335.5
CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked 220.438 209.118 11.32
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted Divided 128.909 120.173 1.0727
FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Ranked 220.437 209.118 1.05413
FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Rooted Subtracted 100.169 95.6772 4.4918
SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Measured 5768.32 6434.78 666.46
699 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Ranked 220.438 209.118 11.32
ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Rooted Divided 57.0263 61.1552 1.0724
COQ3 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Squared Subtracted 25626.4 29950.3 4323.9
CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked Divided 220.438 209.118 1.05413
HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Squared 18148.6 21253.1 1.17106
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Measured 7101.94 7949.84 1.11939

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/