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 1113 to 1162 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
557 CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 207.272 194.371 1.06637
SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Subtracted 216.557 230.362 13.805
558 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 248.994 235.255 13.739
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 135.087 144.041 1.06628
559 RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Subtracted 216.72 230.439 13.719
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 207.309 194.452 1.06612
560 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Subtracted 232.118 218.406 13.712
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Divided 205.74 193.021 1.06589
561 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Subtracted 228.215 214.546 13.669
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Divided 205.89 193.183 1.06578
562 GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 220.744 207.121 1.06577
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Subtracted 224.606 210.944 13.662
563 CAPS calcyphosine. [swissprot;acc:q13938] Divided 220.744 207.121 1.06577
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted 224.606 210.944 13.662
564 CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 220.744 207.121 1.06577
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Subtracted 13.623
565 CAPS calcyphosine. [swissprot;acc:q13938]
ZNF547 sedlin. [swissprot;acc:o14582] Divided 129.219 121.261 1.06563
566 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Subtracted 220.744 207.121 13.623
567 RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 228.639 242.258 13.619
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Divided 129.219 121.261 1.06563
568 no value putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 226.3 212.38 1.06554
SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Subtracted 228.639 242.258 13.619
569 GPKOW t54 protein. [swissprot;acc:q92917] Divided 226.3 212.38 1.06554
PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Subtracted 228.639 242.258 13.619
570 SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Divided 229.709 215.631 1.06529
SNX17 sorting nexin 17. [swissprot;acc:q15036] Subtracted 228.639 242.258 13.619
571 MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Divided 238.529 254.099 1.06528
MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 221.807 208.264 13.543
572 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Divided 227.86 213.945 1.06504
DNAJB11 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Subtracted 221.807 208.264 13.543
573 GNL2 autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 13.485
GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Divided 227.86 213.945 1.06504
574 MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 221.807 208.264 1.06503
POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Subtracted 237.554 250.823 13.269
575 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 13.146
DNAJB11 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Divided 221.807 208.264 1.06503
576 no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 1.0648
POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Subtracted 232.469 245.613 13.144
577 PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 224.606 210.944 1.06477
RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] Subtracted 217.862 230.978 13.116
578 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 15 28 13
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Divided 224.606 210.944 1.06477
579 PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted 15 28 13
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Divided 246.805 231.796 1.06475
580 PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 15 28 13
ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Divided 236.751 252.038 1.06457
581 PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 15 28 13
TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Divided 237.28 252.492 1.06411

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/