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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1151 to 1200 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
576 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 235.18 250.419 1.0648
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 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 13.116
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 224.606 210.944 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 15 28 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 224.606 210.944 1.06477
579 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted 15 28 13
zinc finger protein t86. [swissprot;acc:o00488] Divided 246.805 231.796 1.06475
580 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 15 28 13
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 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 15 28 13
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Divided 237.28 252.492 1.06411
582 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted 15 28 13
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Divided 237.28 252.492 1.06411
583 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Subtracted 233.725 220.751 12.974
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Divided 237.28 252.492 1.06411
584 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Subtracted 233.725 220.751 12.974
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Divided 237.28 252.492 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 207.222 194.262 12.96
586 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Divided 237.28 252.492 1.06411
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 217.215 204.279 12.936
587 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Divided 237.28 252.492 1.06411
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Subtracted 217.67 230.596 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 216.557 230.362 1.06375
589 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 217.67 230.596 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 228.215 214.546 1.06371
590 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Subtracted 217.67 230.596 12.926
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 217.215 204.279 1.06333
591 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Subtracted 217.67 230.596 12.926
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Divided 216.72 230.439 1.0633
592 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Subtracted 217.67 230.596 12.926
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 91.63 97.4011 1.06298
593 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Subtracted 217.67 230.596 12.926
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided 232.118 218.406 1.06278
594 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 207.26 194.346 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 212.2 199.849 1.0618
596 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Subtracted 207.26 194.346 12.914
vav-3 protein. [swissprot;acc:q9ukw4] Divided 212.253 199.908 1.06175
597 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 207.26 194.346 12.914
vav-2 protein. [swissprot;acc:p52735] Divided 212.526 200.212 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 207.261 194.347 12.914
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 248.463 234.095 1.06138
599 crk-like protein. [swissprot;acc:p46109] Subtracted 207.26 194.346 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 248.463 234.095 1.06138
600 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Subtracted 207.26 194.346 12.914
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Divided 248.463 234.095 1.06138

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/