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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1150 to 1199 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
575 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
588 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Divided 230.362 216.557 1.06375
589 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 230.596 217.67 12.926
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Divided 214.546 228.215 1.06371
590 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Subtracted 230.596 217.67 12.926
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 204.279 217.215 1.06333
591 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Subtracted 230.596 217.67 12.926
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Divided 230.439 216.72 1.0633
592 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Subtracted 230.596 217.67 12.926
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 97.4011 91.63 1.06298
593 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Subtracted 230.596 217.67 12.926
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided 218.406 232.118 1.06278
594 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 210.136 223.282 1.06256
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 194.346 207.26 12.914
595 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
vav proto-oncogene. [swissprot;acc:p15498] Divided 199.849 212.2 1.0618
596 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Subtracted 194.346 207.26 12.914
vav-3 protein. [swissprot;acc:q9ukw4] Divided 199.908 212.253 1.06175
597 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 194.346 207.26 12.914
vav-2 protein. [swissprot;acc:p52735] Divided 200.212 212.526 1.0615
598 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] Subtracted 194.347 207.261 12.914
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 234.095 248.463 1.06138
599 crk-like protein. [swissprot;acc:p46109] Subtracted 194.346 207.26 12.914
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Divided 234.095 248.463 1.06138
600 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Subtracted 194.346 207.26 12.914

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/