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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2130 to 2179 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
267 no value estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared Subtracted 59334.6 68040.1 8705.5
ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted Divided 66.1064 74.1073 1.12103
CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured Subtracted 11222.2 9948.93 1273.27
DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked Divided 241.07 267.88 1.11121
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 26157.6 20236.2 1.29261
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 11523 1.21682
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Subtracted 61.2893 70.3856 9.0963
268 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Divided 66.1064 74.1074 1.12103
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 24473.9 20127.8 1.21593
CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Subtracted 11222.2 9948.93 1273.27
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked Divided 271.016 244.167 1.10996
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 26157.6 20236.2 1.29261
PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked Subtracted 241.625 265.136 23.511
SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 35533.9 44227 8693.1
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 61.2893 70.3856 9.0963
269 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Ranked 241.625 265.136 23.511
ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 35508.7 44191.4 8682.7
BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured 4808.79 6074.21 1265.42
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] Rooted 61.2893 70.3856 9.0963
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 66.1064 74.1074 1.12103
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 5575.52 1.21466
PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked 241.373 267.352 1.10763
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 26157.6 20236.2 1.29261
270 C16orf80 transcription factor iib. [refseq;acc:nm_013242] 64739.9 50300.6 1.28706
CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured Subtracted 4810.22 6075.04 1264.82
CRKL crk-like protein. [swissprot;acc:p46109] Rooted Divided 66.1064 74.1074 1.12103
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358
FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked 241.373 267.352 1.10763
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared Subtracted 35508.6 44191.3 8682.7
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 241.612 265.119 23.507
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 9.007
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 Divided 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
COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared Subtracted 53774.6 45105.5 8669.1
COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 8.9859
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured 4812.01 6076.09 1264.08
SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 23.487
SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared Divided 64739.9 50300.6 1.28706
272 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Rooted Subtracted 57.4432 66.3307 8.8875
FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared Divided 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
MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured 1991.03 3221.38 1230.35
SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared 35247.5 43820.5 8573
273 AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 30826.5 39383.9 8557.4
CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted 57.45 66.332 8.882
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Divided 3199.4 3870.8 1.20985

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/