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 Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2625 to 2674 of 66312 in total
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
165 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] RPL6 Subtracted Ranked Low confidence 209.954 221.607 11.653
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 Divided 222.508 210.345 1.05782
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] GAD2 High confidence 209.299 249.187 1.19058
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Subtracted Measured 4489.19 2765.82 1723.37
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Divided Squared 173408 242989 1.40126
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Rooted 55.6486 65.1478 1.1707
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Measured 23693.7 18263 1.29736
monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] SLC16A8 Low confidence 10341.7 11198.5 1.08285
musashi 1. [refseq;acc:nm_002442] MSI1 Subtracted Rooted High confidence 54.9787 66.2416 11.2629
nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Divided Squared Low confidence 37094.3 41487.9 1.11844
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] PLAA Subtracted Measured 11162 10526.2 635.8
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] PCSK5 Squared 54208.6 48413.8 5794.8
septin 6. [swissprot;acc:q14141] SEPT6 Divided Rooted 97.7187 104.263 1.06697
spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Subtracted Ranked High confidence 133 105 28
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] CLEC3B Squared 59016.1 75486.9 16470.8
tho complex 3. [refseq;acc:nm_032361] no value Rooted Low confidence 72.7219 77.3133 4.5914
166 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 Measured 9012.1 8376.35 635.75
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] CTBP2 Squared High confidence 69201.8 53013.4 16188.4
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] CAPN2 Divided Ranked Low confidence 222.502 210.342 1.05781
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP Subtracted Squared 53479.8 47812.1 5667.7
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG Divided Ranked High confidence 209.299 249.187 1.19058
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL Subtracted Measured 4489.19 2765.82 1723.37
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Divided Squared 173408 242989 1.40126
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Rooted 55.6495 65.1458 1.17064
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Measured 23693.7 18263 1.29736
monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] SLC16A3 Low confidence 10325 11178.2 1.08263
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Subtracted Ranked High confidence 312 284 28
nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Rooted 54.9787 66.2416 11.2629
transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Divided Squared Low confidence 37094.3 41487.9 1.11844
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] TNS3 Subtracted Ranked 219.336 207.703 11.633
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] TP53I3 Rooted 87.7928 92.3802 4.5874
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C Divided 72.46 77.3071 1.06689
167 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 Subtracted Ranked High confidence 133 105 28
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 Squared 64975.9 81151.2 16175.3
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 Divided Low confidence 23804.2 26534 1.11468
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Measured 12376.5 11436.5 1.08219
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] FLNB Subtracted Rooted High confidence 55.6161 66.7332 11.1171
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 Divided Ranked 209.299 249.187 1.19058
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Squared 173408 242989 1.40126
homeobox protein nkx-6.1. [swissprot;acc:p78426] NKX6-1 Subtracted Low confidence 64485.5 70068.3 5582.8
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Divided Rooted High confidence 55.65 65.1448 1.17062
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Measured 23693.7 18263 1.29736
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A Subtracted 4489.19 2765.82 1723.37
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Rooted Low confidence 70.7428 75.3259 4.5831
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 Divided Ranked 212.695 201.131 1.05749
Rooted 68.0417 72.5283 1.06594
Subtracted Ranked 212.695 201.131 11.564
vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Measured 7497.17 8131.56 634.39
168 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] BCL6B Squared High confidence 69165.6 52992.1 16173.5
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 Divided Rooted Low confidence 72.4531 77.213 1.0657

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/