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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 762 to 811 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
381 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 1 200.586 183.423 1.09357
382 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 0 10449 10061.8 1.03848
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] 1 200.791 183.66 1.09328
383 chromodomain y-like protein 2. [refseq;acc:nm_152342] 0 10273.1 10665.1 1.03816
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 1 237.862 217.739 1.09242
384 bystin. [swissprot;acc:q13895] 0 10833.3 11244.5 1.03796
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] 1 266.421 244.236 1.09083
385 testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 0 10302.7 10686.7 1.03727
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 0 10303.7 10687.4 1.03724
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 1 242.238 264.11 1.09029
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 0 10481.8 10869.5 1.03699
388 peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 9953.39 10320.9 1.03692
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 1 227.575 208.756 1.09015
389 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 0 11794.7 11375.4 1.03686
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 1 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
alpha-nac protein. [sptrembl;acc:q9h009] 0 14204.4 14724.5 1.03662
391 40s ribosomal protein s16. [swissprot;acc:p17008] 1 241.828 263.62 1.09011
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 14223.9 14738.5 1.03618
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 1 241.83 263.615 1.09008
seven in absentia homolog 1. [refseq;acc:nm_003031] 0 9854.67 10201.4 1.03518
393 spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 1 225.719 207.072 1.09005
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 0 12576 13010 1.03451
394 60s ribosomal protein l12. [swissprot;acc:p30050] 10196.9 9857.79 1.0344
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 1 218.827 238.407 1.08948
395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 0 10195.5 9856.7 1.03437
396 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 10194.8 9856.12 1.03436
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 1 240.801 262.34 1.08945
397 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 0 10006.9 9676.53 1.03414
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1 110.689 101.613 1.08932
398 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 0 16699.2 17267.9 1.03406
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 1 218.818 238.358 1.0893
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 226.226 1.08821
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 0 16703.1 17271.4 1.03402
400 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 16711 17278.4 1.03395
phosducin-like protein (phlp). [swissprot;acc:q13371] 1 207.908 226.218 1.08807
401 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 0 12305.9 11904.9 1.03368
402 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 10562.4 10918 1.03367
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 1 207.908 226.218 1.08807
403 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 0 9783.63 10111.2 1.03348
404 dna repair protein rad52 homolog. [swissprot;acc:p43351] 1 207.908 226.218 1.08807
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 0 9783.63 10111.2 1.03348
405 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 1 207.931 226.209 1.0879
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 0 9783.63 10111.2 1.03348
406 glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]

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/