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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1286 to 1335 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
161 Subtracted MYH13 Measured myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 9035 1755.4 7279.6
NEUROD1 Ranked neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 312 28 284
TRMU Squared trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 52591.3 17253.8 69845.1
162 Divided HNRNPR Rooted heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 52.7642 1.17318 61.9019
HOXC5 Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 173408 1.40126 242989
MAGEB6B Measured melanoma antigen, family b, 6. [refseq;acc:nm_173523] 23693.7 1.29736 18263
NOSTRIN Ranked nostrin. [refseq;acc:nm_052946] 209.299 1.19058 249.187
Subtracted no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 28 170
CLEC11A Squared stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 59704 16756.4 76460.4
HMG20A Measured high-mobility group 20a. [refseq;acc:nm_018200] 5140.14 1753.39 6893.53
KCNIP2 Rooted kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 43.4554 11.6978 31.7576
163 Divided no value Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 23693.7 1.29736 18263
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 173408 1.40126 242989
EIF4G1 Rooted eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 52.7702 1.17285 61.8915
SNF8 Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 209.299 1.19058 249.187
Subtracted ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 28 105
CLEC3A Squared c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 59464 16656.8 76120.8
CSTF2T Measured likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 14976.4 1729.8 13246.6
NCBP2 Rooted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 11.6751 66.6101
164 Divided HOXD4 Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 173408 1.40126 242989
MAGEA9 Measured melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 23693.7 1.29736 18263
MXD1 Rooted mad protein (max dimerizer). [swissprot;acc:q05195] 55.646 1.17086 65.1534
SLC39A6 Ranked liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 209.299 1.19058 249.187
Subtracted ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 133 28 105
DUT Squared deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 61733.5 16509.4 45224.1
GBE1 Measured 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 1723.37 2765.82
MSI2 Rooted musashi 2 isoform a. [refseq;acc:nm_138962] 54.9787 11.2629 66.2416
165 Divided GAD2 Ranked glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 209.299 1.19058 249.187
HOXB5 Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 173408 1.40126 242989
MAGEA8 Measured melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 23693.7 1.29736 18263
MXI1 Rooted max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 55.6486 1.1707 65.1478
Subtracted CLEC3B Squared tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 59016.1 16470.8 75486.9
MSI1 Rooted musashi 1. [refseq;acc:nm_002442] 54.9787 11.2629 66.2416
PYGB Measured glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 4489.19 1723.37 2765.82
SPATA6 Ranked spermatogenesis associated 6. [refseq;acc:nm_019073] 133 28 105
166 Divided HOXA5 Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 173408 1.40126 242989
MAGEC1 Measured melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 23693.7 1.29736 18263
MXD4 Rooted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 55.6495 1.17064 65.1458
NAPG Ranked gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 1.19058 249.187
Subtracted CTBP2 Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 69201.8 16188.4 53013.4
NEUROD4 Ranked neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 28 284
PYGL Measured glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 1723.37 2765.82
ZC3H14 Rooted nuclear protein ukp68. [refseq;acc:nm_024824] 54.9787 11.2629 66.2416
167 Divided no value Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 173408 1.40126 242989
GAD1 Ranked glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 1.19058 249.187
MAGEA4 Measured melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 23693.7 1.29736 18263
RAB24 Rooted max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 55.65 1.17062 65.1448
Subtracted AMPD2 Ranked amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 133 28 105
CANT1 Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 16175.3 81151.2
FLNB Rooted 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] 55.6161 11.1171 66.7332

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/