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 Value Type description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 12912 in total
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
Value Type
description
red
green
network_comparison
388 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
Squared mad protein (max dimerizer). [swissprot;acc:q05195] 17248.4 21214 1.22991
Rooted pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 58.6533 64.5958 1.10132
395 Measured splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 4532.73 5269.33 1.16251
Ranked dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 218.827 238.407 1.08948
Squared max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 17254.4 21218.1 1.22972
Rooted protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 50.0423 45.4523 1.10098
396 Measured ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 6563.65 7627.29 1.16205
Ranked putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 240.801 262.34 1.08945
Squared max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 17256.5 21219.6 1.22966
Rooted a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 116.797 106.111 1.10071
397 Measured nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 5367.04 6233.12 1.16137
Ranked t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 110.689 101.613 1.08932
Squared max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 17257.5 21220.3 1.22963
Rooted raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 116.792 106.107 1.1007
398 Measured xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 5084.26 5904.1 1.16125
Ranked muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 1.0893
Squared imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 18929.1 23222.8 1.22683
Rooted serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 116.707 106.044 1.10055
399 Measured neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 5201.41 4479.76 1.16109
Ranked clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 226.226 1.08821
Squared microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 18929.1 23222.8 1.22683
Rooted cyclin g2. [swissprot;acc:q16589] 116.707 106.044 1.10055
400 Measured adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 5201.41 4479.76 1.16109
Ranked phosducin-like protein (phlp). [swissprot;acc:q13371] 207.908 226.218 1.08807
Squared glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 39478.8 48419 1.22646
Rooted cyclin g1 (cyclin g). [swissprot;acc:p51959] 116.707 106.044 1.10055

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/