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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1633 to 1682 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
409 DOK2 Measured docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 6102.59 7081.46 1.1604
HTRA1 Squared serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 18995.6 23242.8 1.22359
MRPL3 Rooted mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 50.4409 45.8795 1.09942
POLR1E Ranked rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 1.08641
410 no value 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] 233.376 253.539 1.0864
BCAR1 Squared crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 19546.1 23881.6 1.22181
DOK1 Measured docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 6102.59 7081.46 1.1604
PAH Rooted phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 55.5489 50.535 1.09922
411 DUS1L pp3111 protein. [refseq;acc:nm_022156]
FRK Measured tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 6102.59 7081.46 1.1604
GTF2H1 Ranked tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 233.376 253.539 1.0864
SNRPD3 Squared small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 17861.2 21821.8 1.22174
412 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 19556 23891.8 1.22171
MKI67IP Measured 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
STX18 Rooted syntaxin 18. [swissprot;acc:q9p2w9] 55.5489 50.535 1.09922
UQCRFSL1 Ranked ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 240.788 261.416 1.08567
413 no value Rooted rd protein. [swissprot;acc:p18615] 55.5489 50.535 1.09922
NEDD9 Squared 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] 19568.3 23904.6 1.2216
POLR1C Ranked dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
VAV1 Measured vav proto-oncogene. [swissprot;acc:p15498] 6644.99 7707.8 1.15994
414 ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
DPM1 Squared 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] 22109.6 26989.4 1.22071
GSTO1 Rooted glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 55.5489 50.535 1.09922
KATNA1 Ranked katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 252.238 1.08522
415 AIG1 Rooted androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 55.5489 50.535 1.09922
KATNB1 Ranked katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 232.382 252.166 1.08514
SORBS3 Squared vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 29160.4 35570.2 1.21981
VAV3 Measured vav-3 protein. [swissprot;acc:q9ukw4] 6647.43 7706.18 1.15927
416 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 4509.54 5223.95 1.15842
ATP5F1 Rooted atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 55.5489 50.535 1.09922
PHB Squared prohibitin. [swissprot;acc:p35232] 22841.8 27856.2 1.21953
POLR1B Ranked dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 240.6 261.041 1.08496
417 no value Squared repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 22841.8 27856.2 1.21953
BAG3 Measured 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] 4522.71 5233.14 1.15708
DNAJC12 Rooted j domain containing protein 1. [swissprot;acc:q9ukb3] 55.5489 50.535 1.09922
SETMAR Ranked set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 253.197 1.08417
418 BCAS2 Measured breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 5493.1 6350.19 1.15603
CLEC4M Ranked cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 233.539 253.197 1.08417
ENOPH1 Squared e-1 enzyme. [refseq;acc:nm_021204] 30903.8 37638.1 1.21791
SNX13 Rooted sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 55.5489 50.535 1.09922
419 APOA1BP Squared apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 24832.1 30242.8 1.21789
CDC5L Measured 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] 5493.1 6350.19 1.15603
FCER2 Ranked low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 233.539 253.197 1.08417
GSTO2 Rooted ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 55.5489 50.535 1.09922
420 CD209 Ranked cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 233.539 253.197 1.08417
HPRT1 Measured hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 10235.2 11830.8 1.15589
POLE Rooted dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 51.7959 56.9253 1.09903
RPL24 Squared 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 30924.3 37652.3 1.21756
421 no value Rooted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 50.4666 45.9317 1.09873
CBL Squared cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 36933 44953.6 1.21717

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
- Hugo is the HGNC identifier if it exists
- 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/