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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
100 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Rooted Divided High confidence 0 20.0501 15.3244 1.30838
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared Subtracted Low confidence 16325.5 13564.1 2761.4
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] High confidence 310373 311745 1372
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked Divided 1 88.2482 110.265 1.24949
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Squared Low confidence 0 0.70501 1.50296 2.13183
monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Subtracted 1 63904 72791.6 8887.6
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Rooted Divided 63.7749 69.4515 1.08901
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 High confidence 0 492.157 225.924 2.17842
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Ranked Subtracted Low confidence 11725.7 13865.5 2139.8
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted Divided High confidence 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
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Measured Divided Low confidence 5752.65 6330.03 1.10037
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted Subtracted High confidence 19.9625 35.798 15.8355
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 61.9982 68.2337 6.2355
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Divided 0 5.47723 7.07107 1.29099
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Measured 817.81 551.434 1.48306
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Squared 1 70019.5 82296.2 1.17533
zinc finger protein 117 (zinc finger protein hpf9) (fragment). [swissprot;acc:q03924] Measured Subtracted 0 2352.42 1969.43 382.99
zinc finger protein 277. [swissprot;acc:q9nrm2] Ranked Divided 8725.56 10626.9 1.2179
zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523] Rooted Subtracted 45.3043 40.7113 4.593
101 60s ribosomal protein l37a. [swissprot;acc:p12751] Measured Divided 535.61 362.955 1.47569
b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2] Squared 27.0961 12.7302 2.12849
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] High confidence 1 222655 143584 1.5507
coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Ranked Subtracted Low confidence 226.395 211.713 14.682
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] High confidence 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
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Rooted Low confidence 13.7191 17.6786 1.28861
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Subtracted High confidence 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
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Ranked Subtracted Low confidence 0 7923.89 10030.4 2106.51
leucine zipper domain protein. [refseq;acc:nm_024589] Divided 1 221.996 238.82 1.07579
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted High confidence 0 12.6886 9.74679 1.30182
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 1 88.2482 110.265 1.24949
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured Subtracted Low confidence 10685.5 11612.9 927.4
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked High confidence 204.641 161.051 43.59
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured Divided 0 1442 977 1.47595
raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] Squared Low confidence 1 63526.9 54384.3 1.16811
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted Subtracted 68.4921 74.6877 6.1956
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Measured High confidence 14924.4 17655.2 2730.8
septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 35900.4
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Measured Divided Low confidence 5752.65 6330.03 1.10037
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Ranked 0 8703.84 10598.3 1.21766
solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Squared Subtracted 1 63903.1 72790.2 8887.1
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 0 9225.25 11941.1 2715.85
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Divided High confidence 956.375 441.285 2.16725

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/