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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
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
network_comparison
green
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 1.16769 14889.2
378 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 15034.5 1.23398 18552.2
MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 1.10263 45.8738
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured 12471.7 1.16758 14561.7
RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 1.09387 265.365
379 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 1.23391 40732.2
AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 1.0938 264.163
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 59.5128 1.10235 65.604
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured 6704.44 1.16512 7811.45
380 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked 242.109 1.09368 264.79
ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 1.16461 15138.2
ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared 32991.5 1.23379 40704.5
CAPS calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 1.10235 65.604
381 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared 32987.4 1.23376 40698.5
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 1.10235 65.604
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 1.16456 6109.31
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Ranked 200.586 1.09357 183.423
382 no value rna-binding protein. [refseq;acc:nm_019027] Squared 15043.7 1.23375 18560.1
PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured 4533.74 1.16447 5279.4
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Rooted 49.8325 1.1023 45.2077
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 1.09328 183.66
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 1.23375 18560.1
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured 4533.74 1.16447 5279.4
MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Rooted 49.8325 1.1023 45.2077
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 237.862 1.09242 217.739
384 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Rooted 50.7723 1.10229 46.0607
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 1.16447 5279.4
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 1.09083 244.236
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Squared 15043.7 1.23375 18560.1
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 1.10229 46.0607
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 1.09083 244.236
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared 15043.7 1.23375 18560.1
PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Measured 4533.74 1.16447 5279.4
386 no value scratch; scratch 1. [refseq;acc:nm_031309] Squared 40388.9 1.23369 49827.5
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Rooted 50.0513 1.10215 45.4124
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Measured 4533.74 1.16447 5279.4
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Ranked 242.238 1.09029 264.11
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 1.10209 45.6718
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared 15053 1.23351 18568
HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Measured 4533.74 1.16447 5279.4
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 1.23318 49716.4
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked 227.575 1.09015 208.756
HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Measured 4533.74 1.16447 5279.4
SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted 50.3345 1.10209 45.6718
389 DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Measured 4533.74 1.16447 5279.4
RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Squared 31819.7 1.23264 39222.2
RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted 50.3345 1.10209 45.6718
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked 227.575 1.09015 208.756
390 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 1.23108 35572.8

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/