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 Network Comparison Type description Value Type red Interaction Map green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 2375 to 2424 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
Value Type
red
green
network_comparison
297 Subtracted mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 196.978 22.443
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted 66.1064 74.1073 8.0009
298 Divided calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Ranked 268.632 243.588 1.10281
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Squared 14247.4 18142.1 1.27336
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted 57.6823 64.4212 1.11683
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 5572.85 1.20262
Subtracted adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1137.66
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Squared 28901.4 36762.1 7860.7
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 66.1064 74.1073 8.0009
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Ranked 266.421 244.236 22.185
299 Divided ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Measured 4914.27 5907.12 1.20203
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked 268.635 243.592 1.10281
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 28896.2 36767 1.27238
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 1.11638
Subtracted coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Squared 51527.6 43689.1 7838.5
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] Rooted 66.1063 74.1068 8.0005
metaxin 1. [swissprot;acc:q13505] Measured 9327.58 10442.2 1114.62
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Ranked 266.421 244.236 22.185
300 Divided metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 166.351 1.10196
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted 48.1584 53.7378 1.11586
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 28896.2 36767 1.27238
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured 4914.27 5907.12 1.20203
Subtracted coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Squared 51527.6 43689.1 7838.5
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Rooted 43.5479 51.5473 7.9994
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked 257.017 234.945 22.072
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Measured 4446.72 5553.79 1107.07
301 Divided beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Ranked 150.982 166.372 1.10193
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured 13768.2 11466 1.20078
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] Rooted 203.673 182.638 1.11517
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 28896.2 36767 1.27238
Subtracted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Rooted 66.1048 74.0977 7.9929
coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Squared 51527.6 43689.1 7838.5
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Ranked 88.2482 110.265 22.0168
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured 4446.72 5553.79 1107.07
302 Divided 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted 203.673 182.638 1.11517
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured 5894.75 7073.65 1.19999
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 28896.2 36767 1.27238
Subtracted coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 51527.6 43689.1 7838.5
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked 88.2482 110.265 22.0168
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted 66.1046 74.0964 7.9918
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured 6704.44 7811.45 1107.01
303 Divided 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 22268.8 18560.4 1.1998
Subtracted melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked 88.2482 110.265 22.0168
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 7838.5
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 62.9007 70.8854 7.9847
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Measured 4723.53 5828.46 1104.93

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/