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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 Hugo description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1162 to 1211 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
581 TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Divided 237.28 252.492 1.06411
582 BARX1 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted 15 28 13
583 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 233.725 220.751 12.974
OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Divided 237.28 252.492 1.06411
584 BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Subtracted 233.725 220.751 12.974
TLX2 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 TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Subtracted 207.222 194.262 12.96
586 HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Divided 237.28 252.492 1.06411
RRM1 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 BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Divided 237.28 252.492 1.06411
HRB 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 no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Divided 216.557 230.362 1.06375
589 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] 228.215 214.546 1.06371
PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 217.67 230.596 12.926
590 no value intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
RRM1 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 HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Subtracted 217.67 230.596 12.926
RPP30 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 C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Subtracted 217.67 230.596 12.926
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 91.63 97.4011 1.06298
593 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
HTATSF1 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
594 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Divided 223.282 210.136 1.06256
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 207.26 194.346 12.914
595 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Divided 212.2 199.849 1.0618
596 no value 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
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Divided 212.253 199.908 1.06175
597 HCK 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
VAV2 vav-2 protein. [swissprot;acc:p52735] Divided 212.526 200.212 1.0615
598 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
GRAP2 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
599 AKT3 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
CRKL crk-like protein. [swissprot;acc:p46109] Subtracted 207.26 194.346 12.914
600 ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
AKT2 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
601 FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Subtracted 207.26 194.346 12.914
VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Divided 206.274 218.792 1.06069
602 FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Subtracted 207.26 194.346 12.914
MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Divided 206.274 218.792 1.06069
603 CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Subtracted 207.27 194.368 12.902
LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Divided 225.829 212.945 1.0605
604 CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Subtracted 207.272 194.371 12.901
RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] Divided 217.862 230.978 1.0602
605 HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 247.47 233.441 1.0601
LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Subtracted 225.829 212.945 12.884
606 HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Divided 247.47 233.441 1.0601

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/