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.


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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1527 to 1576 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
382 RPS23 Rooted 40s ribosomal protein s23. [swissprot;acc:p39028] 49.8325 45.2077 1.1023
TAF7L 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
383 no value Measured hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 4533.74 5279.4 1.16447
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
MRPS12 Rooted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 49.8325 45.2077 1.1023
RBM39 Ranked rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
384 no value Measured cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 4533.74 5279.4 1.16447
Rooted 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 50.7723 46.0607 1.10229
E2F1 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
SYNCRIP Squared ns1-associated protein 1. [refseq;acc:nm_006372] 15043.7 18560.1 1.23375
385 BCCIP 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
E2F2 Ranked transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 266.421 244.236 1.09083
HNRNPR Squared heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 15043.7 18560.1 1.23375
PSIP1 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
386 no value Squared scratch; scratch 1. [refseq;acc:nm_031309] 40388.9 49827.5 1.23369
EIF1B Rooted protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 50.0513 45.4124 1.10215
RPL8 Measured 60s ribosomal protein l8. [swissprot;acc:p25120] 4533.74 5279.4 1.16447
RPS14 Ranked 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
387 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
Rooted 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 50.3345 45.6718 1.10209
EIF4G1 Squared eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 15053 18568 1.23351
HDGF Measured hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 4533.74 5279.4 1.16447
388 no value 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
HDGFL1 Measured pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 4533.74 5279.4 1.16447
SRR Rooted serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 50.3345 45.6718 1.10209
389 DDX6 Measured probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 4533.74 5279.4 1.16447
RARS2 Squared arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 31819.7 39222.2 1.23264
RPL34 Rooted 60s ribosomal protein l34. [swissprot;acc:p49207] 50.3345 45.6718 1.10209
SNRPF Ranked small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 227.575 208.756 1.09015
390 no value Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 28895.6 35572.8 1.23108
MRPL13 Ranked 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
SEC61A2 Rooted protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 50.3345 45.6718 1.10209
TMEM131 Measured rw1 protein (fragment). [swissprot;acc:q92545] 4533.74 5279.4 1.16447
391 KPNB1 Squared importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 28895.6 35572.8 1.23108
RPS16 Ranked 40s ribosomal protein s16. [swissprot;acc:p17008] 241.828 263.62 1.09011
SEC61A1 Rooted protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 50.3345 45.6718 1.10209
TARDBP Measured tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 3658.76 3144.39 1.16358
392 DDX54 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
RPL13A Ranked 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 241.83 263.615 1.09008
RPL3L Rooted 60s ribosomal protein l3-like. [swissprot;acc:q92901] 50.3313 45.6913 1.10155
TBL1X Squared transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] 28895.6 35572.8 1.23108
393 EIF4E 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
POLR2A Rooted dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 49.8842 45.2875 1.1015
TBL1Y Squared transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 28895.6 35572.8 1.23108
TXNL4A 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
394 BAIAP3 Measured bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 4490.28 5222.25 1.16301
CDC40 Rooted pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 58.6533 64.5958 1.10132
DPP9 Ranked dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 218.827 238.407 1.08948
MXD1 Squared mad protein (max dimerizer). [swissprot;acc:q05195] 17248.4 21214 1.22991

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/