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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1125 to 1174 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
563 calcyphosine. [swissprot;acc:q13938] Divided 207.121 220.744 1.06577
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted 210.944 224.606 13.662
564 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 207.121 220.744 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 121.261 129.219 1.06563
566 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Subtracted 207.121 220.744 13.623
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 121.261 129.219 1.06563
567 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Subtracted 242.258 228.639 13.619
bet3 homolog. [swissprot;acc:o43617] Divided 121.261 129.219 1.06563
568 putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 212.38 226.3 1.06554
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Subtracted 242.258 228.639 13.619
569 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
t54 protein. [swissprot;acc:q92917] Divided 212.38 226.3 1.06554
570 sorting nexin 17. [swissprot;acc:q15036] Subtracted 242.258 228.639 13.619
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Divided 215.631 229.709 1.06529
571 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 254.099 238.529 1.06528
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 208.264 221.807 13.543
572 cbf1 interacting corepressor. [refseq;acc:nm_004882] Divided 213.945 227.86 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 208.264 221.807 13.543
573 autoantigen ngp-1. [swissprot;acc:q13823] 236.817 250.302 13.485
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Divided 213.945 227.86 1.06504
574 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Subtracted 250.823 237.554 13.269
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided 208.264 221.807 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 210.136 223.282 13.146
576 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 250.419 235.18 1.0648
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Subtracted 245.613 232.469 13.144
577 60s ribosomal protein l15. [swissprot;acc:p39030] 230.978 217.862 13.116
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 210.944 224.606 1.06477
578 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] Subtracted 28 15 13
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Divided 210.944 224.606 1.06477
579 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted 28 15 13
zinc finger protein t86. [swissprot;acc:o00488] Divided 231.796 246.805 1.06475
580 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 28 15 13
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Divided 252.038 236.751 1.06457
581 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 28 15 13
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Divided 252.492 237.28 1.06411
582 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted 28 15 13
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Divided 252.492 237.28 1.06411
583 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Subtracted 220.751 233.725 12.974
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Divided 252.492 237.28 1.06411
584 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Subtracted 220.751 233.725 12.974
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Divided 252.492 237.28 1.06411
585 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Subtracted 194.262 207.222 12.96
586 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Divided 252.492 237.28 1.06411
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 204.279 217.215 12.936
587 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Divided 252.492 237.28 1.06411
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Subtracted 230.596 217.67 12.926

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/