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.


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 Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2201 to 2250 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Value Type
red
network_comparison
green
551 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] CDIPT Squared 27516.2 1.18912 32720
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] GABRA3 Rooted 66.082 1.0843 71.6525
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] GRAP2 Ranked 207.261 1.06645 194.347
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] no value Measured 5773.45 1.13687 6563.69
552 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] ARFGAP1 Squared 27516.2 1.18912 32720
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] CSTF2 Measured 15427.2 1.13663 13572.8
crk-like protein. [swissprot;acc:p46109] CRKL Ranked 207.26 1.06645 194.346
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] NDUFA6 Rooted 66.082 1.08429 71.6523
553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Ranked 207.26 1.06645 194.346
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] PDXDC1 Rooted 66.082 1.08429 71.6523
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] no value Measured 3853.64 1.13651 4379.71
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] VAMP3 Squared 27516.2 1.18912 32720
554 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] HOXD9 Rooted 66.0829 1.08419 71.6462
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] CLP1 Measured 14830.5 1.13641 13050.3
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Squared 8426.68 1.18799 10010.8
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Ranked 207.26 1.06645 194.346
555 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] SKP1A Squared 8426.68 1.18799 10010.8
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 Measured 6167.93 1.13615 7007.7
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 Rooted 59.7823 1.08376 64.7895
556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Ranked 207.27 1.06638 194.368
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] FBXW7 Squared 8426.68 1.18799 10010.8
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2 Measured 6167.93 1.13615 7007.7
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Rooted 66.0911 1.08345 71.6061
557 cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 Squared 8426.68 1.18799 10010.8
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Ranked 207.272 1.06637 194.371
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B Measured 6167.93 1.13615 7007.7
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Rooted 97.1967 1.08339 105.302
558 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 66.1583 1.08335 71.6729
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 Squared 8426.68 1.18799 10010.8
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1 Measured 6167.93 1.13615 7007.7
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value Ranked 135.087 1.06628 144.041
559 cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 Squared 8426.68 1.18799 10010.8
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] FTH1 Rooted 62.7397 1.08329 67.9651
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A Measured 6167.93 1.13615 7007.7
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL Ranked 207.309 1.06612 194.452
560 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] CBS Measured 5480.24 1.13536 6222.04
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] ETFDH Squared 26334.7 1.18749 31272.3
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] no value Rooted 51.0687 1.08325 47.1439
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] SOS1 Ranked 205.74 1.06589 193.021
561 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] CREG2 Rooted 62.7424 1.08324 67.9648
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] SOS2 Ranked 205.89 1.06578 193.183
transforming protein rhoc (h9). [swissprot;acc:p08134] RHOC Measured 5480.24 1.13536 6222.04
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 Squared 18240.1 1.18745 21659.2
562 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] no value Rooted 62.7424 1.08324 67.9648
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] FBP2 Squared 25294.9 1.18709 30027.4
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] GULP1 Ranked 220.744 1.06577 207.121
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] TST Measured 5480.24 1.13536 6222.04
563 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST
calcyphosine. [swissprot;acc:q13938] CAPS Ranked 220.744 1.06577 207.121

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/