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 4658 to 4707 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
583 cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted Subtracted 60.0587 65.0057 4.947
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Squared 31994 36719.6 4725.6
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Ranked 233.725 220.751 12.974
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Measured 6834.54 7590.49 755.95
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Divided 6739.81 7644.62 1.13425
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Ranked 237.28 252.492 1.06411
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Rooted 121.695 131.815 1.08316
584 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Squared 23526.4 27879.3 1.18502
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Ranked Subtracted 233.725 220.751 12.974
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Rooted 60.0587 65.0057 4.947
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Squared 31989.3 36713.2 4723.9
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Measured Divided 6739.82 7644.63 1.13425
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Rooted 104.459 113.143 1.08313
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Ranked 237.28 252.492 1.06411
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Measured Subtracted 6834.54 7590.49 755.95
585 40s ribosomal protein s11. [swissprot;acc:p04643] Rooted 50.4705 45.5342 4.9363
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Squared 25287.7 30003.7 4716
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Measured Divided 6739.82 7644.63 1.13425
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Squared 23526.4 27879.3 1.18502
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Rooted 51.5667 55.8498 1.08306
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Ranked 237.28 252.492 1.06411
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Measured Subtracted 6834.54 7590.49 755.95
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Ranked 207.222 194.262 12.96
586 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted 50.3167 45.4063 4.9104
alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Squared Divided 23526.4 27879.3 1.18502
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Measured Subtracted 6139.04 6893.7 754.66
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Rooted Divided 51.5667 55.8498 1.08306
hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Ranked 237.28 252.492 1.06411
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Measured 6739.81 7644.62 1.13425
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Squared Subtracted 23512.2 28206.2 4694
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Ranked 217.215 204.279 12.936
587 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Measured 6772.75 7526.2 753.45
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Rooted Divided 51.7204 56.0156 1.08305
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Measured 6739.83 7644.63 1.13425
homeobox protein barh-like 2. [swissprot;acc:q9umq3] Ranked 237.28 252.492 1.06411
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Squared Subtracted 23512.2 28206.2 4694
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Divided 23526.5 27879.4 1.18502
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Ranked Subtracted 217.67 230.596 12.926
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Rooted 69.2869 74.1856 4.8987
588 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Squared Divided 23526.4 27879.3 1.18502
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Subtracted 23512.2 28206.2 4694
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Measured Divided 6739.83 7644.63 1.13425
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Rooted 59.7294 64.6872 1.083
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Ranked Subtracted 217.67 230.596 12.926
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Divided 216.557 230.362 1.06375
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Rooted Subtracted 69.3627 74.2575 4.8948
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Measured 6691.93 7445.09 753.16
589 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Rooted 82.0749 86.9643 4.8894
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 15465.1 20151 4685.9
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Rooted Divided 59.7294 64.6872 1.083

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/