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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2951 to 3000 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
369 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Squared 0 346.699 309.317 1.12085
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Rooted 17.8274 17.1002 1.04253
370 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 30.7424 32.0298 1.04188
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Measured 1049.21 989.438 1.06041
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 1 4108.15 4808.93 1.17058
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Rooted 49.7435 45.0586 1.10397
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 1.09475
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared 45986 56776.1 1.23464
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Ranked 0 13652.7 13061 1.0453
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Squared 1039.56 927.649 1.12064
371 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 1 45985.9 56776 1.23464
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 0 18585 20796.3 1.11898
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Measured 1631.97 1542.23 1.05819
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Rooted 20.9428 21.8063 1.04123
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Ranked 1 186.52 170.42 1.09447
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Measured 5067.02 5926.46 1.16961
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Ranked 0 13247.9 12674.2 1.04527
zinc finger-like protein 9. [refseq;acc:nm_033414] Rooted 1 49.3451 54.4606 1.10367
372 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Squared 45986.7 56776.8 1.23464
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Measured 0 5427.25 5130.58 1.05782
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Ranked 11869.9 12402.7 1.04489
enigma protein; lim domain protein. [refseq;acc:nm_005451] Squared 21.836 19.5177 1.11878
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted 1 49.3451 54.4606 1.10367
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Measured 5067 5926.17 1.16956
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 186.52 170.42 1.09447
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted 0 11.9476 12.4394 1.04116
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked 1 242.37 265.255 1.09442
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared 45986 56776.1 1.23464
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Rooted 49.3451 54.4606 1.10367
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 0 2713.5 2864.68 1.05571
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Ranked 10598.2 11061.5 1.04371
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured 1 5066.99 5926.1 1.16955
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 0 30.3054 31.5389 1.0407
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 215.107 192.635 1.11666
374 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted 1 50.2549 45.5599 1.10305
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Measured 0 2323.8 2452.23 1.05527
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared 2572.14 2869.96 1.11579
calcyphosine. [swissprot;acc:q13938] Ranked 9874.54 9478.1 1.04183
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 30.2858 31.5117 1.04048
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured 1 5066.93 5925.38 1.16942
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 45987 56777.1 1.23463
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 267.208 244.168 1.09436
375 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 1.23463
60s ribosomal protein l35. [swissprot;acc:p42766] Rooted 50.2545 45.5637 1.10295
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked 242.686 265.516 1.09407
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Measured 0 2323.8 2452.23 1.05527
germ cell-less. [refseq;acc:nm_022471] Rooted 27.8491 26.7806 1.0399
importin 9. [refseq;acc:nm_018085] Squared 1062.18 952.74 1.11487
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Ranked 14247.6 13686.9 1.04097
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 1 4700.42 5492.63 1.16854

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/