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 Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1625 to 1674 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
407 Measured WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 6603.41 7664.65 1.16071
Ranked MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
Squared HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 18995.7 23244.9 1.22369
Rooted no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 49.9856 45.4431 1.09996
408 Measured dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
Ranked CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
Squared HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 18995.7 23244.7 1.22368
Rooted no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 49.9856 45.4432 1.09996
409 Measured DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 6102.59 7081.46 1.1604
Ranked POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 1.08641
Squared HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 18995.6 23242.8 1.22359
Rooted MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 50.4409 45.8795 1.09942
410 Measured DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 6102.59 7081.46 1.1604
Ranked 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
Squared BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 19546.1 23881.6 1.22181
Rooted PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 55.5489 50.535 1.09922
411 Measured FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 6102.59 7081.46 1.1604
Ranked 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] 233.376 253.539 1.0864
Squared SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 17861.2 21821.8 1.22174
Rooted DUS1L pp3111 protein. [refseq;acc:nm_022156] 55.5489 50.535 1.09922
412 Measured MKI67IP 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
Ranked UQCRFSL1 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
Squared 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
Rooted STX18 syntaxin 18. [swissprot;acc:q9p2w9] 55.5489 50.535 1.09922
413 Measured VAV1 vav proto-oncogene. [swissprot;acc:p15498] 6644.99 7707.8 1.15994
Ranked POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
Squared 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] 19568.3 23904.6 1.2216
Rooted no value rd protein. [swissprot;acc:p18615] 55.5489 50.535 1.09922
414 Measured ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
Ranked KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 252.238 1.08522
Squared 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] 22109.6 26989.4 1.22071
Rooted GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 55.5489 50.535 1.09922
415 Measured VAV3 vav-3 protein. [swissprot;acc:q9ukw4] 6647.43 7706.18 1.15927
Ranked KATNB1 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
Squared SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 29160.4 35570.2 1.21981
Rooted AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 55.5489 50.535 1.09922
416 Measured ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 4509.54 5223.95 1.15842
Ranked POLR1B 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
Squared PHB prohibitin. [swissprot;acc:p35232] 22841.8 27856.2 1.21953
Rooted ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 55.5489 50.535 1.09922
417 Measured BAG3 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
Ranked SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 253.197 1.08417
Squared no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 22841.8 27856.2 1.21953
Rooted DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] 55.5489 50.535 1.09922
418 Measured BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 5493.1 6350.19 1.15603
Ranked CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 233.539 253.197 1.08417
Squared ENOPH1 e-1 enzyme. [refseq;acc:nm_021204] 30903.8 37638.1 1.21791
Rooted SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 55.5489 50.535 1.09922
419 Measured CDC5L 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
Ranked FCER2 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

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/