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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1613 to 1662 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
404 ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 26819.1 32855.4 1.22507
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured 5201.41 4479.76 1.16109
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 59.6834 65.6741 1.10037
RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 226.218 1.08807
405 ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Squared 26822.2 32858.1 1.22503
BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Rooted 116.576 105.948 1.10031
CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked 207.931 226.209 1.0879
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Measured 5201.41 4479.76 1.16109
406 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted 49.9858 45.4433 1.09996
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 265.634 244.304 1.08731
HTRA2 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Squared 18995.7 23245.6 1.22373
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Measured 5201.41 4479.76 1.16109
407 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 1.09996
HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Squared 18995.7 23244.9 1.22369
MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Ranked 239.75 260.544 1.08673
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Measured 6603.41 7664.65 1.16071
408 no value 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
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 1.08649
HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Squared 18995.7 23244.7 1.22368
409 DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured 6102.59 7081.46 1.1604
HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Squared 18995.6 23242.8 1.22359
MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Rooted 50.4409 45.8795 1.09942
POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] Ranked 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 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Squared 19546.1 23881.6 1.22181
DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Measured 6102.59 7081.46 1.1604
PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Rooted 55.5489 50.535 1.09922
411 DUS1L pp3111 protein. [refseq;acc:nm_022156]
FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Measured 6102.59 7081.46 1.1604
GTF2H1 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
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Squared 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 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Measured 3594.31 4169.95 1.16015
STX18 syntaxin 18. [swissprot;acc:q9p2w9] Rooted 55.5489 50.535 1.09922
UQCRFSL1 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 no value rd protein. [swissprot;acc:p18615] Rooted 55.5489 50.535 1.09922
NEDD9 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
POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Ranked 240.913 261.45 1.08525
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Measured 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 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
GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted 55.5489 50.535 1.09922
KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Ranked 232.431 252.238 1.08522
415 AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Rooted 55.5489 50.535 1.09922
KATNB1 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
SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared 29160.4 35570.2 1.21981
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Measured 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 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Rooted 55.5489 50.535 1.09922

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/