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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
green
red
network_comparison
201 chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted Subtracted High confidence 0 30.2263 33.0227 2.7964
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 1 127.926 138.375 10.449
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked Divided Low confidence 219.23 208.591 1.051
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared Subtracted High confidence 0 113.017 468.221 355.204
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted Divided Low confidence 1 75.4476 71.1262 1.06076
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] High confidence 70.3856 61.2893 1.14842
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Squared Low confidence 47103.2 52176.8 1.10771
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Rooted High confidence 0 20.9336 23.8722 1.14038
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Ranked 15123 16853 1.1144
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted Subtracted Low confidence 5.80678 9.84765 4.04087
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared High confidence 1 55802.1 42411.6 13390.5
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Measured Low confidence 0 0 286 286
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 1 74.7299 70.4583 4.2716
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured High confidence 0 6856.28 6699.82 156.46
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted Divided Low confidence 51.8401 58.6947 1.13223
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 18590.6 13924.6 1.33509
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked High confidence 1 211.382 240.133 1.13601
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Measured 0 5690.63 6804.88 1.1958
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1 6075.04 4810.22 1.26294
tenascin n precursor (fragment). [sptrembl;acc:q9uqp3] Squared Subtracted Low confidence 47095 52163.9 5068.9
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured High confidence 12069.5 10603.5 1466
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Ranked Low confidence 214.089 203.935 10.154
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 14788.5 13555.3 1233.2
zinc finger protein 180 (hhz168). [swissprot;acc:q9ujw8] Measured Divided 1967.99 2350.86 1.19455
zinc finger protein 197 (znf20). [swissprot;acc:o14709] Ranked 4848.21 4251.62 1.14032
202 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted 1 75.377 71.0652 1.06067
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Subtracted High confidence 266.079 240.758 25.321
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 0 8.12243 10.9038 2.78137
aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Measured Low confidence 1 9814.59 9246.23 568.36
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] High confidence 0 2194.52 2039.07 155.45
brca1 associated protein. [refseq;acc:nm_006768] Low confidence 1403.03 1117.36 285.67
calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence 1 12069.5 10603.5 1466
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 95434.8 71030.1 1.34358
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 0 723.75 606.049 1.19421
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared Subtracted Low confidence 15071.5 13985 1086.5
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided High confidence 2360.97 3339.18 1.41433
dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Ranked Subtracted Low confidence 1 168.371 178.507 10.136
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 Divided High confidence 6076.09 4812.01 1.26269
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked Low confidence 222.252 211.51 1.05079
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Rooted High confidence 0 20.9336 23.8722 1.14038
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted Low confidence 5.80678 9.84765 4.04087
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared High confidence 1 55802.1 42411.6 13390.5
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Divided Low confidence 50139.7 55537.3 1.10765
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Rooted 0 29.9209 33.8758 1.13218
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 1 9682.99 10391.8 1.0732
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Squared 0 31089.6 23310.5 1.33372
serpin b11. [swissprot;acc:q96p15] Ranked High confidence 15123 16853 1.1144
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1 228.784 201.478 1.13553
similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_033196] Low confidence 0 4848.21 4251.62 1.14032
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Subtracted 1 75.3451 71.0886 4.2565

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/