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 1630 to 1679 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
408 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Rooted 49.9856 45.4432 1.09996
dok-like protein. [refseq;acc:nm_024872] Measured 6102.59 7081.46 1.1604
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Squared 18995.7 23244.7 1.22368
409 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured 6102.59 7081.46 1.1604
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Rooted 50.4409 45.8795 1.09942
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Ranked 241.045 261.874 1.08641
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Squared 18995.6 23242.8 1.22359
410 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 19546.1 23881.6 1.22181
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Measured 6102.59 7081.46 1.1604
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Rooted 55.5489 50.535 1.09922
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Ranked 233.376 253.539 1.0864
411 pp3111 protein. [refseq;acc:nm_022156] Rooted 55.5489 50.535 1.09922
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Squared 17861.2 21821.8 1.22174
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Ranked 233.376 253.539 1.0864
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Measured 6102.59 7081.46 1.1604
412 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 3594.31 4169.95 1.16015
syntaxin 18. [swissprot;acc:q9p2w9] Rooted 55.5489 50.535 1.09922
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Squared 19556 23891.8 1.22171
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Ranked 240.788 261.416 1.08567
413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Squared 19568.3 23904.6 1.2216
rd protein. [swissprot;acc:p18615] Rooted 55.5489 50.535 1.09922
vav proto-oncogene. [swissprot;acc:p15498] Measured 6644.99 7707.8 1.15994
414 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Squared 22109.6 26989.4 1.22071
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted 55.5489 50.535 1.09922
katanin p60 subunit a 1. [refseq;acc:nm_007044] Ranked 232.431 252.238 1.08522
415 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Rooted 55.5489 50.535 1.09922
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Ranked 232.382 252.166 1.08514
vav-3 protein. [swissprot;acc:q9ukw4] Measured 6647.43 7706.18 1.15927
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared 29160.4 35570.2 1.21981
416 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Rooted 55.5489 50.535 1.09922
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Ranked 240.6 261.041 1.08496
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Measured 4509.54 5223.95 1.15842
prohibitin. [swissprot;acc:p35232] Squared 22841.8 27856.2 1.21953
417 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Measured 4522.71 5233.14 1.15708
j domain containing protein 1. [swissprot;acc:q9ukb3] Rooted 55.5489 50.535 1.09922
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Squared 22841.8 27856.2 1.21953
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Ranked 233.539 253.197 1.08417
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Measured 5493.1 6350.19 1.15603
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Ranked 233.539 253.197 1.08417
e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 1.21791
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Rooted 55.5489 50.535 1.09922
419 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Squared 24832.1 30242.8 1.21789
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Rooted 55.5489 50.535 1.09922
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Measured 5493.1 6350.19 1.15603
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 233.539 253.197 1.08417
420 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared 30924.3 37652.3 1.21756
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Ranked 233.539 253.197 1.08417
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Rooted 51.7959 56.9253 1.09903

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/