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.


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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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7541 to 7590 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1886 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Ranked 204.512 206.682 1.01061
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] Rooted 69.8124 71.8658 1.02941
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Measured 5826 6195.48 1.06342
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Squared 26276.4 28767.6 1.09481
1887 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] Rooted 69.8109 71.8643 1.02941
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Measured 5438.6 5783.11 1.06335
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Squared 26276.4 28767.6 1.09481
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Ranked 220.896 218.577 1.01061
1888 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Measured 5438.6 5783.11 1.06335
c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] Rooted 62.2848 64.1142 1.02937
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Ranked 218.414 216.131 1.01056
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Squared 26276.4 28767.6 1.09481
1889 60s ribosomal protein l30. [swissprot;acc:p04645] 12981.1 14211.2 1.09476
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Rooted 64.3493 66.2289 1.02921
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Ranked 211.27 209.067 1.01054
testis-specific bromodomain protein. [refseq;acc:nm_001726] Measured 5438.68 5783.2 1.06335
1890 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Squared 12685.5 13884.4 1.09451
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Rooted 65.3912 67.3008 1.0292
nag14 protein. [refseq;acc:nm_022143] Measured 5438.6 5783.11 1.06335
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Ranked 211.314 209.111 1.01054
1891 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Measured 5438.18 5782.62 1.06334
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Rooted 65.3912 67.3008 1.0292
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared 24776.1 27116.5 1.09446
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Ranked 233.828 231.395 1.01051
1892 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] Measured 5438.52 5783.01 1.06334
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Ranked 233.828 231.395 1.01051
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Rooted 65.3912 67.3008 1.0292
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Squared 24776.2 27116.2 1.09445
1893 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Measured 6830.4 7261.98 1.06319
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Ranked 222.842 225.17 1.01045
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Squared 12646.6 13840 1.09437
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Rooted 61.9751 63.7825 1.02916
1894 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 52.8726 54.4127 1.02913
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Measured 3598.08 3384.59 1.06308
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Ranked 222.842 225.17 1.01045
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Squared 12567.5 13752.3 1.09427
1895 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 12581.2 13765.5 1.09413
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Ranked 215.853 213.639 1.01036
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Rooted 65.1861 67.0846 1.02912
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Measured 5882.1 6252.66 1.063
1896 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Rooted 63.4427 65.2881 1.02909
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Ranked 199.883 197.835 1.01035
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Measured 4521 4805.16 1.06285
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Squared 12581.2 13765.5 1.09413
1897 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Ranked 199.883 197.835 1.01035
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Measured 4590.74 4879.11 1.06282
transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] Squared 46338.5 42353.5 1.09409
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Rooted 63.4353 65.2789 1.02906
1898 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Measured 6885.11 7317.48 1.0628
lim/homeobox protein lhx4. [swissprot;acc:q969g2] Ranked 199.881 197.833 1.01035

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/