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 [...,...].
Gene Rank Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Value Type
Interaction Map
red
green
network_comparison
270 FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked High confidence 241.373 267.352 1.10763
RNF10 ring finger protein 10. [refseq;acc:nm_014868] Low confidence 208.437 199.44 1.04511
UTP3 disrupter of silencing 10. [refseq;acc:nm_020368] Squared 51294.5 47142.5 1.08807
271 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked High confidence 241.373 267.352 1.10763
ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 66.1064 74.1073 1.12103
CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 3093.78 1.21092
CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 8811.69 9345.26 1.06055
PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 51583 47416 1.08788
SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] High confidence 64739.9 50300.6 1.28706
SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Rooted Low confidence 65.1441 68.7656 1.05559
TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Ranked 201.219 192.595 1.04478
272 ALDH4A1 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Measured 11162 10526.2 1.0604
AP2A2 adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973] Rooted 70.162 74.0605 1.05556
FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared High confidence 36563.7 46971.1 1.28464
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 74.1074 1.12103
HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 3858.52 4669.27 1.21012
LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 241.373 267.352 1.10763
OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Low confidence 217.69 208.421 1.04447
PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 51555.9 47412 1.0874
273 CDC73 parafibromin. [refseq;acc:nm_024529] Ranked 214.015 204.916 1.0444
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured High confidence 3199.4 3870.8 1.20985
FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 74.1074 1.12103
FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Squared 16120.1 20665.7 1.28198
HOOK3 golgi-associated microtubule-binding protein hook3; hook3 protein. [refseq;acc:nm_032410] Low confidence 49860 45859.7 1.08723
PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked High confidence 241.373 267.352 1.10763
PLAA phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Measured Low confidence 11162 10526.2 1.0604
PUF60 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Rooted 70.162 74.0605 1.05556
274 AP2S1 clathrin coat assembly protein ap17 (clathrin coat associated protein ap17) (plasma membrane adaptor ap-2 17 kda protein) (ha2 17 kda subunit) (clathrin assembly protein 2 small chain). [swissprot;acc:p53680]
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] High confidence 66.1063 74.1068 1.12102
HOOK1 hook1 protein. [refseq;acc:nm_015888] Squared Low confidence 49842 45846.9 1.08714
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 209.532 200.653 1.04425
POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] High confidence 241.373 267.352 1.10763
RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Measured 3119.98 2579.49 1.20953
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Squared 16120.1 20665.7 1.28198
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured Low confidence 7718.85 8184.75 1.06036
275 no value adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782] Rooted 70.162 74.0605 1.05556
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] High confidence 66.1048 74.0977 1.12091
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured Low confidence 7506.19 7958.12 1.06021
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 199.66 191.203 1.04423
PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] High confidence 241.373 267.352 1.10763
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared 16120.1 20665.7 1.28198
RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Measured 3119.98 2579.49 1.20953
TTK dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981] Squared Low confidence 47648.2 43829.4 1.08713
276 CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted High confidence 66.1046 74.0964 1.1209
DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Low confidence 70.9492 74.89 1.05554
HOOK2 hook2 protein. [refseq;acc:nm_013312] Squared 49837.9 45843.9 1.08712
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked 199.939 191.474 1.04421
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Squared High confidence 16120.1 20665.7 1.28198
RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Measured 3119.98 2579.49 1.20953
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Ranked 241.13 266.969 1.10716

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/