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 1101 to 1150 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
551 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Divided 207.261 194.347 1.06645
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Subtracted 222.156 208.201 13.955
552 crk-like protein. [swissprot;acc:p46109] Divided 207.26 194.346 1.06645
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Subtracted 222.156 208.201 13.955
553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 207.26 194.346 1.06645
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Subtracted 226.3 212.38 13.92
554 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 207.26 194.346 1.06645
t54 protein. [swissprot;acc:q92917] Subtracted 226.3 212.38 13.92
555 cbf1 interacting corepressor. [refseq;acc:nm_004882] 227.86 213.945 13.915
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 207.26 194.346 1.06645
556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 1.06638
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Subtracted 227.86 213.945 13.915
557 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 207.272 194.371 1.06637
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Subtracted 216.557 230.362 13.805
558 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 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 207.309 194.452 1.06612
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
560 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Divided 205.74 193.021 1.06589
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Subtracted 232.118 218.406 13.712
561 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Divided 205.89 193.183 1.06578
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
562 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 224.606 210.944 13.662
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided 220.744 207.121 1.06577
563 calcyphosine. [swissprot;acc:q13938]
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 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 220.744 207.121 1.06577
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Subtracted 13.623
565 calcyphosine. [swissprot;acc:q13938]
sedlin. [swissprot;acc:o14582] Divided 129.219 121.261 1.06563
566 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Subtracted 220.744 207.121 13.623
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 129.219 121.261 1.06563
567 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Subtracted 228.639 242.258 13.619
bet3 homolog. [swissprot;acc:o43617] Divided 129.219 121.261 1.06563
568 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
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 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
t54 protein. [swissprot;acc:q92917] Divided 226.3 212.38 1.06554
570 sorting nexin 17. [swissprot;acc:q15036] Subtracted 228.639 242.258 13.619
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Divided 229.709 215.631 1.06529
571 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 238.529 254.099 1.06528
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 221.807 208.264 13.543
572 cbf1 interacting corepressor. [refseq;acc:nm_004882] Divided 227.86 213.945 1.06504
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 autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 13.485
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Divided 227.86 213.945 1.06504
574 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Subtracted 237.554 250.823 13.269
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided 221.807 208.264 1.06503
575 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]
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted 223.282 210.136 13.146

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/