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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1560 to 1609 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
98 pp3111 protein. [refseq;acc:nm_022156] Measured Divided 0 789 530 1.48868
Squared 147.342 66.4852 2.21616
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 1 2353.63 3225.65 1.3705
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Subtracted 204.641 160.957 43.684
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 36304.3
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Rooted Divided 0 13.2903 17.4395 1.3122
transcription factor lbx1. [swissprot;acc:p52954] 1 47.6504 36.9304 1.29028
trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked Subtracted 0 11520.7 13680.4 2159.7
99 brain protein 44. [swissprot;acc:o95563] Squared 1 89182.8 125229 36046.2
dystrophin. [swissprot;acc:p11532] Measured 0 427.217 111.739 315.478
jun dimerization protein. [refseq;acc:nm_130469] Ranked 1 204.641 160.957 43.684
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 0 12787.8 10454.7 1.22316
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Rooted Subtracted 27.8028 22.9122 4.8906
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Squared Divided 492.157 225.924 2.17842
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked Subtracted 7584.72 9706.12 2121.4
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Rooted Divided 31.495 24.0263 1.31086
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Measured 1 2353.63 3225.65 1.3705
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 15999.1 19007.1 3008
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 19.9625 35.798 15.8355
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Measured Divided 0 817.81 551.434 1.48306
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Squared Subtracted 19277.3 20652.4 1375.1
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided 1 226186 145568 1.55382
100 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Measured 0 594 402 1.47761
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Rooted Subtracted 22.4608 17.665 4.7958
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Squared Divided 1 226186 145568 1.55382
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Ranked 0 9183.49 11217.7 1.22151
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Measured Subtracted 2698.62 3010.22 311.6
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Ranked 12584.5 10470.6 2113.9
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Measured Divided 1 2353.63 3225.65 1.3705
fos-related antigen 2. [swissprot;acc:p15408] Ranked Subtracted 204.641 161.046 43.595
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Rooted Divided 0 20.0501 15.3244 1.30838
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Squared Subtracted 310373 311745 1372
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked Divided 1 88.2482 110.265 1.24949
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Squared 0 492.157 225.924 2.17842
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 1 47.6504 36.9304 1.29028
septin 6. [swissprot;acc:q14141] Measured Subtracted 15959.9 18957.1 2997.2
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 125229 36046.2
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted 19.9625 35.798 15.8355
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Divided 222655 143584 1.5507
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Ranked Subtracted 0 12577.8 14662.1 2084.3
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured Divided 1 2353.63 3225.65 1.3705
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted Subtracted 19.9625 35.798 15.8355
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked Divided 0 14548.5 11915.2 1.221
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Rooted Subtracted 34.3021 29.5305 4.7716
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Squared 5294.83 3966.41 1328.42
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 638.862 330.189 308.673
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted Divided 1 47.6504 36.9304 1.29028

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/