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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 751 to 800 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
376 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Subtracted 248.152 267.226 19.074
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Divided 257.017 234.945 1.09395
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 242.691 265.481 1.09391
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Subtracted 248.152 267.226 19.074
378 60s ribosomal protein l30. [swissprot;acc:p04645] Divided 242.593 265.365 1.09387
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Subtracted 248.152 267.226 19.074
379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Divided 241.509 264.163 1.0938
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Subtracted 248.152 267.226 19.074
380 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Divided 242.109 264.79 1.09368
381 thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted 248.152 267.226 19.074
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 183.423 1.09357
382 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 253.852 234.808 19.044
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] Divided 200.791 183.66 1.09328
383 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 237.862 217.739 1.09242
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Subtracted 236.245 255.113 18.868
384 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 227.575 208.756 18.819
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] Divided 266.421 244.236 1.09083
385 small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 227.575 208.756 18.819
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 266.421 244.236 1.09083
386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 1.09029
40s ribosomal protein s9. [swissprot;acc:p46781] Subtracted 238.986 257.784 18.798
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Divided 242.238 264.11 1.09029
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 56.6768 75.3531 18.6763
388 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 56.7244 75.3948 18.6704
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Divided 227.575 208.756 1.09015
389 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 56.7252 75.3954 18.6702
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 56.7841 75.447 18.6629
391 40s ribosomal protein s16. [swissprot;acc:p17008] Divided 241.828 263.62 1.09011
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 225.719 207.072 18.647
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 241.83 263.615 1.09008
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Subtracted 239.092 257.705 18.613
393 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 238.921 257.327 18.406
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 225.719 207.072 1.09005
394 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 207.889 226.226 18.337
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 218.827 238.407 1.08948
395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
phosducin-like protein (phlp). [swissprot;acc:q13371] Subtracted 207.908 226.218 18.31
396 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Divided 240.801 262.34 1.08945
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] Subtracted 207.908 226.218 18.31
397 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 110.689 101.613 1.08932
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 1.0893
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted 207.908 226.218 18.31
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 207.889 226.226 1.08821
dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 207.908 226.218 18.31
400 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 18.278
phosducin-like protein (phlp). [swissprot;acc:q13371] Divided 207.908 226.218 1.08807

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/