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 3858 to 3907 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
483 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Squared 0 312092 313482 1.00445
histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted 1 50.6084 55.2961 1.09263
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured 9649.61 11053.5 1.14549
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 0 20612.9 20672.6 1.0029
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Ranked 1 237.109 254.667 1.07405
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Squared 26867.3 32335.2 1.20352
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Ranked 0 12223.8 12127.5 1.00794
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 1 237.109 254.667 1.07405
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] Squared 0 311980 313369 1.00445
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Rooted 1 50.6084 55.2961 1.09263
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Measured 9649.61 11053.5 1.14549
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked 0 11489.7 11414.3 1.00661
scribble. [refseq;acc:nm_015356] Measured 958.429 961.098 1.00278
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Squared 1 26867.2 32335 1.20351
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Rooted 0 24.2134 24.1232 1.00374
485 60s ribosomal protein l18. [swissprot;acc:q07020] Ranked 1 237.109 254.667 1.07405
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Rooted 0 26.4223 26.5172 1.00359
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Measured 22850.1 22797.8 1.00229
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Squared 310884 312261 1.00443
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Ranked 12461.5 12542.3 1.00648
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Squared 1 26867.2 32335 1.20351
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Measured 9649.61 11053.5 1.14549
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Rooted 50.6084 55.2961 1.09263
486 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 0 20.6398 20.7123 1.00351
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Squared 310373 311745 1.00442
histone h2b.e (h2b/e). [swissprot;acc:q99879] Rooted 1 50.6084 55.2961 1.09263
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 0 13372.4 13288.3 1.00633
mct-1 protein. [refseq;acc:nm_014060] 1 226.313 243.03 1.07387
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Measured 0 22878.7 22826.8 1.00227
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared 1 26865.9 32332.9 1.20349
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 10908.6 12491.8 1.14513
487 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared 0 68035.1 68294.1 1.00381
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Ranked 1 226.313 243.03 1.07387
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Rooted 0 12.5028 12.4629 1.0032
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Measured 1 5277.4 6042.88 1.14505
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 0 250.419 249.857 1.00225
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared 1 26865.9 32332.9 1.20349
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Ranked 0 13236.8 13159.3 1.00589
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Rooted 1 50.0015 54.627 1.09251
488 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured 10872.4 12447 1.14483
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Squared 0 5487.61 5469.34 1.00334
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Rooted 25.44 25.3889 1.00201
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 1 50.4315 46.1703 1.09229
heat shock factor binding protein 1. [swissprot;acc:o75506] Ranked 0 15204.2 15127.8 1.00505
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Measured 250.419 249.857 1.00225
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared 1 26866.1 32333.2 1.20349
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Ranked 225.026 209.798 1.07258
489 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted 50.5505 46.2797 1.09228
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Measured 0 22946.3 22895.1 1.00224
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Rooted 22.997 22.9676 1.00128

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/