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.


Navigation/Query Panel:
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 Hugo description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
307 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured Divided 12365.2 14824.9 1.19892
GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Squared 28896.4 36766.8 1.27237
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked Subtracted 88.2482 110.265 22.0168
SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted Divided 50.4687 45.2733 1.11476
SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 1.10126
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted Subtracted 66.0989 74.0609 7.962
308 ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared 32991.5 40704.5 7713
AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Divided 30596.2 38919.9 1.27205
BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Measured Subtracted 11852.9 10773.5 1079.4
DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Rooted Divided 50.4687 45.2733 1.11476
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 1.19878
NDN necdin. [swissprot;acc:q99608] Ranked Subtracted 88.2482 110.265 22.0168
RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Divided 242.153 266.673 1.10126
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Rooted Subtracted 65.9938 73.9449 7.9511
309 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Divided 56.185 62.6036 1.11424
AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Squared Subtracted 32987.4 40698.5 7711.1
BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Measured 11848.8 10770.3 1078.5
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared Divided 28900.8 36762.6 1.27203
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured 4977.8 5966.14 1.19855
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked Subtracted 88.2482 110.265 22.0168
SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Divided 242.153 266.673 1.10126
310 no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Measured Subtracted 7551.8 8630.06 1078.26
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted Divided 95.0526 85.3206 1.11406
C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared Subtracted 30651.3 38253.3 7602
CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 28901.4 36762.1 1.27198
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked Subtracted 88.2482 110.265 22.0168
SART1 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] Measured Divided 4909.79 5878.79 1.19736
SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 242.153 266.673 1.10126
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Rooted Subtracted 56.9506 64.7888 7.8382
311 no value 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 7500.7
AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Divided 30566.4 38866.5 1.27154
APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Measured Subtracted 2820.51 3897.1 1076.59
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 4981.52 5964.58 1.19734
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 242.627 267.151 1.10108
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Subtracted 88.2482 110.265 22.0168
MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted Divided 95.0526 85.3206 1.11406
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Subtracted 62.3337 70.0738 7.7401
312 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 88.2482 110.265 22.0168
methyltransferase like 2. [refseq;acc:nm_018396] Squared Divided 71576.8 56326.7 1.27074
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 1.19622
DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared Subtracted 33044.3 40524.8 7480.5
MAX max protein. [swissprot;acc:p25912] Measured 4640.26 5704.87 1064.61
MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted Divided 95.0526 85.3206 1.11406
NOSTRIN nostrin. [refseq;acc:nm_052946] Subtracted 59.6399 51.9242 7.7157
RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked Divided 242.195 266.663 1.10103
313 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 1.27074
FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Subtracted 45189.6 52666.2 7476.6
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Measured 4567.04 5631.2 1064.16
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 88.2482 110.265 22.0168

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/