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.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1508 to 1557 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
377 PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 14889.2 1.16769
378 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 15034.5 18552.2 1.23398
MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 1.10263
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured 12471.7 14561.7 1.16758
RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 265.365 1.09387
379 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 1.23391
AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 264.163 1.0938
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 59.5128 65.604 1.10235
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured 6704.44 7811.45 1.16512
380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked 242.109 264.79 1.09368
ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 15138.2 1.16461
ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared 32991.5 40704.5 1.23379
CAPS calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 1.10235
381 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared 32987.4 40698.5 1.23376
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 65.604 1.10235
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Measured 5246.01 6109.31 1.16456
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Ranked 200.586 183.423 1.09357
382 no value rna-binding protein. [refseq;acc:nm_019027] Squared 15043.7 18560.1 1.23375
PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured 4533.74 5279.4 1.16447
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Rooted 49.8325 45.2077 1.1023
TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Ranked 200.791 183.66 1.09328
383 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Squared 15043.7 18560.1 1.23375
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured 4533.74 5279.4 1.16447
MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Rooted 49.8325 45.2077 1.1023
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 237.862 217.739 1.09242
384 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Rooted 50.7723 46.0607 1.10229
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 5279.4 1.16447
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Ranked 266.421 244.236 1.09083
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Squared 15043.7 18560.1 1.23375
385 BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Rooted 50.7723 46.0607 1.10229
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 244.236 1.09083
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared 15043.7 18560.1 1.23375
PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Measured 4533.74 5279.4 1.16447
386 no value scratch; scratch 1. [refseq;acc:nm_031309] Squared 40388.9 49827.5 1.23369
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Rooted 50.0513 45.4124 1.10215
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Measured 4533.74 5279.4 1.16447
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Ranked 242.238 264.11 1.09029
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared 15053 18568 1.23351
HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Measured 4533.74 5279.4 1.16447
388 no value dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Squared 40315.7 49716.4 1.23318
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 208.756 1.09015
HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured 4533.74 5279.4 1.16447
SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted 50.3345 45.6718 1.10209
389 DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured 4533.74 5279.4 1.16447
RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared 31819.7 39222.2 1.23264
RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted 50.3345 45.6718 1.10209
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked 227.575 208.756 1.09015
390 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 1.23108

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/