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.


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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 58674 to 58723 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
4107 no value Ranked 60s ribosomal protein l23a. [swissprot;acc:p29316] Subtracted 207.351 209.511 2.16
ACTN4 Rooted alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 70.6002 72.4771 1.8769
CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Divided 73.8531 75.7826 1.02613
GABRG2 Squared gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Subtracted 45599.4 44436.9 1162.5
SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 42503.2 41384.4 1.02703
TXNDC9 Ranked protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 201.865 199.722 1.01073
ZNF343 Measured novel c2h2 type zinc finger protein. [refseq;acc:nm_024325] Subtracted 9143.34 9323.19 179.85
4108 no value lamin b2. [swissprot;acc:q03252] Divided 8091.66 8263.93 1.02129
Rooted casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 73.9438 75.8757 1.02613
testican-3 precursor. [swissprot;acc:q9bq16] Subtracted 63.6177 61.7418 1.8759
GABRE Squared gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 45599.2 44436.7 1162.5
PSMA6 Ranked proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] 201.196 199.036 2.16
SH3BGR sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Divided 202.688 200.543 1.0107
TPD52 Squared tumor protein d52 (n8 protein). [swissprot;acc:p55327] 46258.5 45041 1.02703
ZNF264 Measured zinc finger protein 264. [swissprot;acc:o43296] Subtracted 9143.34 9323.19 179.85
4109 CDC14C Rooted cdc14 homolog b isoform 2. [refseq;acc:nm_033331] Divided 74.7348 76.6879 1.02613
ELP4 Ranked elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Subtracted 203.907 201.752 2.155
GABRA1 Squared gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 45599.1 44436.6 1162.5
LATS2 Ranked lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Divided 202.688 200.543 1.0107
PHACTR3 Rooted q9h4t4 like. [refseq;acc:nm_080672] Subtracted 71.3501 73.2246 1.8745
TPD52L2 Squared tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Divided 46358.5 45139.5 1.02701
TSG101 Measured tumor susceptibility gene 101 protein. [swissprot;acc:q99816] 8102.29 8274.67 1.02128
ZNF8 zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098] Subtracted 9143.33 9323.18 179.85
4110 ALDH3A2 fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648] Divided 7466.02 7624.66 1.02125
ARIH1 Rooted ariadne-1 protein homolog (ari-1) (ubiquitin-conjugating enzyme e2- binding protein 1) (ubch7-binding protein) (ubcm4-interacting protein) (hhari) (h7-ap2) (hussy-27) (mop-6). [swissprot;acc:q9y4x5] 79.6901 81.7719 1.02612
DYM Ranked dymeclin. [refseq;acc:nm_017653] 202.688 200.543 1.0107
GABRA3 Squared gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Subtracted 45599.1 44436.6 1162.5
MAGI3 Rooted membrane-associated guanylate kinase-related 3. [refseq;acc:nm_152900] 71.3501 73.2246 1.8745
RPL5 Ranked 60s ribosomal protein l5. [swissprot;acc:p46777] 207.337 209.485 2.148
SLC11A1 Squared natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Divided 39593 40662.5 1.02701
ZNF324 Measured zinc finger protein 324 (zinc finger protein zf5128). [swissprot;acc:o75467] Subtracted 9143.34 9323.19 179.85
4111 CRAT Rooted carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Divided 72.0108 73.8914 1.02612
EIF1 Measured protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 7607.3 7768.76 1.02122
EXOSC2 Rooted exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Subtracted 71.233 73.1071 1.8741
GABRG3 Squared gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 45599.6 44437.2 1162.4
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] Divided 31573.7 30743.5 1.027
SH3BGR Ranked sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Subtracted 202.688 200.543 2.145
SH3BGRL sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Divided 1.0107
ZNF93 Measured zinc finger protein 93 (zinc finger protein htf34) (fragment). [swissprot;acc:p35789] Subtracted 9143.35 9323.2 179.85
4112 no value similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_033196] 9143.34 9323.19
Squared interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 45599.6 44437.2 1162.4
C11orf30 Rooted emsy protein. [refseq;acc:nm_020193] Divided 70.1775 72.0094 1.0261
CSDA Squared dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] 46458.1 45237.1 1.02699
DYRK1A Rooted dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Subtracted 70.5954 72.4693 1.8739
LATS1 Ranked lats homolog 1. [refseq;acc:nm_004690] Divided 202.688 200.543 1.0107
LATS2 lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Subtracted 2.145
ZNF274 Measured zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Divided 7951.31 8120.05 1.02122
4113 no value zinc finger protein 95 homolog (zfp-95). [swissprot;acc:q9y2l8] Subtracted 9143.33 9323.18 179.85
Ranked sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Divided 202.688 200.543 1.0107
BDH1 Squared d-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (ec 1.1.1.30) (bdh) (3-hydroxybutyrate dehydrogenase). [swissprot;acc:q02338] 43846.3 42694.5 1.02698

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/