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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1525 to 1574 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
382 Measured parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 4533.74 5279.4 1.16447
Ranked 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] 200.791 183.66 1.09328
Squared rna-binding protein. [refseq;acc:nm_019027] 15043.7 18560.1 1.23375
Rooted 40s ribosomal protein s23. [swissprot;acc:p39028] 49.8325 45.2077 1.1023
383 Measured hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 4533.74 5279.4 1.16447
Ranked rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
Squared apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 15043.7 18560.1 1.23375
Rooted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 49.8325 45.2077 1.1023
384 Measured cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 4533.74 5279.4 1.16447
Ranked 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] 266.421 244.236 1.09083
Squared ns1-associated protein 1. [refseq;acc:nm_006372] 15043.7 18560.1 1.23375
Rooted 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 50.7723 46.0607 1.10229
385 Measured pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 4533.74 5279.4 1.16447
Ranked transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 266.421 244.236 1.09083
Squared heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 15043.7 18560.1 1.23375
Rooted 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] 50.7723 46.0607 1.10229
386 Measured 60s ribosomal protein l8. [swissprot;acc:p25120] 4533.74 5279.4 1.16447
Ranked 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
Squared scratch; scratch 1. [refseq;acc:nm_031309] 40388.9 49827.5 1.23369
Rooted protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 50.0513 45.4124 1.10215
387 Measured hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 4533.74 5279.4 1.16447
Ranked 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 242.238 264.11 1.09029
Squared eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 15053 18568 1.23351
Rooted 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 50.3345 45.6718 1.10209
388 Measured pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 4533.74 5279.4 1.16447
Ranked small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 1.09015
Squared dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 40315.7 49716.4 1.23318
Rooted serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 50.3345 45.6718 1.10209
389 Measured probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 4533.74 5279.4 1.16447
Ranked small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 227.575 208.756 1.09015
Squared arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 31819.7 39222.2 1.23264
Rooted 60s ribosomal protein l34. [swissprot;acc:p49207] 50.3345 45.6718 1.10209
390 Measured rw1 protein (fragment). [swissprot;acc:q92545] 4533.74 5279.4 1.16447
Ranked 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 28895.6 35572.8 1.23108
Rooted protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 50.3345 45.6718 1.10209
391 Measured tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 3658.76 3144.39 1.16358
Ranked 40s ribosomal protein s16. [swissprot;acc:p17008] 241.828 263.62 1.09011
Squared importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 28895.6 35572.8 1.23108
Rooted protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 50.3345 45.6718 1.10209
392 Measured atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 3641.89 4236.95 1.16339
Ranked 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 241.83 263.615 1.09008
Squared transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] 28895.6 35572.8 1.23108
Rooted 60s ribosomal protein l3-like. [swissprot;acc:q92901] 50.3313 45.6913 1.10155
393 Measured eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 4490.28 5222.25 1.16301
Ranked spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 225.719 207.072 1.09005
Squared transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 28895.6 35572.8 1.23108
Rooted dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 49.8842 45.2875 1.1015
394 Measured bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 4490.28 5222.25 1.16301
Ranked dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 218.827 238.407 1.08948

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
- 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/