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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 1112 to 1161 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
556 Subtracted GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 13.915 227.86 213.945
557 Divided CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 1.06637 207.272 194.371
Subtracted SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 13.805 216.557 230.362
558 Divided no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 1.06628 135.087 144.041
Subtracted tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 13.739 248.994 235.255
559 Divided WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 1.06612 207.309 194.452
Subtracted RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 13.719 216.72 230.439
560 Divided SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] 1.06589 205.74 193.021
Subtracted DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 13.712 232.118 218.406
561 Divided SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 1.06578 205.89 193.183
Subtracted 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] 13.669 228.215 214.546
562 Divided GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 1.06577 220.744 207.121
Subtracted PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 13.662 224.606 210.944
563 Divided CAPS calcyphosine. [swissprot;acc:q13938] 1.06577 220.744 207.121
Subtracted SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 13.662 224.606 210.944
564 Divided CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 1.06577 220.744 207.121
Subtracted GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 13.623
565 Divided ZNF547 sedlin. [swissprot;acc:o14582] 1.06563 129.219 121.261
Subtracted CAPS calcyphosine. [swissprot;acc:q13938] 13.623 220.744 207.121
566 Divided no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 1.06563 129.219 121.261
Subtracted CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 13.623 220.744 207.121
567 Divided TRAPPC3 bet3 homolog. [swissprot;acc:o43617] 1.06563 129.219 121.261
Subtracted RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 13.619 228.639 242.258
568 Divided no value putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 1.06554 226.3 212.38
Subtracted SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] 13.619 228.639 242.258
569 Divided GPKOW t54 protein. [swissprot;acc:q92917] 1.06554 226.3 212.38
Subtracted PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 13.619 228.639 242.258
570 Divided SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 1.06529 229.709 215.631
Subtracted SNX17 sorting nexin 17. [swissprot;acc:q15036] 13.619 228.639 242.258
571 Divided MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 1.06528 238.529 254.099
Subtracted MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 13.543 221.807 208.264
572 Divided no value cbf1 interacting corepressor. [refseq;acc:nm_004882] 1.06504 227.86 213.945
Subtracted 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] 13.543 221.807 208.264
573 Divided GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 1.06504 227.86 213.945
Subtracted GNL2 autoantigen ngp-1. [swissprot;acc:q13823] 13.485 250.302 236.817
574 Divided MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 1.06503 221.807 208.264
Subtracted POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 13.269 237.554 250.823
575 Divided 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] 1.06503 221.807 208.264
Subtracted CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 13.146 223.282 210.136
576 Divided no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 1.0648 235.18 250.419
Subtracted POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] 13.144 232.469 245.613
577 Divided PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 1.06477 224.606 210.944
Subtracted RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] 13.116 217.862 230.978
578 Divided SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 1.06477 224.606 210.944
Subtracted 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] 13 15 28
579 Divided ZNF593 zinc finger protein t86. [swissprot;acc:o00488] 1.06475 246.805 231.796
Subtracted PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 13 15 28
580 Divided ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] 1.06457 236.751 252.038
Subtracted PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 13 15 28
581 Divided TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] 1.06411 237.28 252.492

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/