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 1551 to 1600 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
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] Divided 0 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
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 1 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
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 0 10481.8 10869.5 387.7
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided 1 241.828 263.62 1.09011
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Subtracted 0 10449 10061.8 387.2
alpha-nac protein. [sptrembl;acc:q9h009] Divided 14204.4 14724.5 1.03662
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 1 56.7841 75.447 18.6629
391 40s ribosomal protein s16. [swissprot;acc:p17008] Divided 241.828 263.62 1.09011
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 14223.9 14738.5 1.03618
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 1 225.719 207.072 18.647
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 0 10302.7 10686.7 384
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 1 241.83 263.615 1.09008
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Subtracted 239.092 257.705 18.613
seven in absentia homolog 1. [refseq;acc:nm_003031] Divided 0 9854.67 10201.4 1.03518
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Subtracted 10303.7 10687.4 383.7
393 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1 238.921 257.327 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
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
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Subtracted 5540 5921 381
394 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 10196.9 9857.79 1.0344
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 1 207.889 226.226 18.337
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 218.827 238.407 1.08948
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted 0 20875 20495 380
395 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 9566.15 9936.37 370.22
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Divided 1 218.827 238.407 1.08948
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 0 10195.5 9856.7 1.03437
phosducin-like protein (phlp). [swissprot;acc:q13371] Subtracted 1 207.908 226.218 18.31
396 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 0 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
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
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 7769.96 8139.71 369.75
397 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Divided 10006.9 9676.53 1.03414
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Subtracted 1 207.908 226.218 18.31
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 0 9565.54 9935.19 369.65
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 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
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] Subtracted 0 9953.39 10320.9 367.51
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 1 207.908 226.218 18.31
399 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 0 7670 7311 359
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 1 207.889 226.226 1.08821
dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 207.908 226.218 18.31
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Divided 0 16703.1 17271.4 1.03402
400 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted 1 207.931 226.209 18.278
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 0 12581.7 12224.2 357.5
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Divided 16711 17278.4 1.03395
phosducin-like protein (phlp). [swissprot;acc:q13371] 1 207.908 226.218 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/