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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1193 to 1242 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
299 no value Measured ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
CAPN1 Ranked calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 268.635 243.592 1.10281
CRK Squared proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 28896.2 36767 1.27238
DVL3 Rooted segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 59.026 65.8955 1.11638
300 ABL2 Squared tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 28896.2 36767 1.27238
MKI67IP Rooted mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 48.1584 53.7378 1.11586
PITRM1 Ranked metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 166.351 1.10196
SNRPA1 Measured u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 4914.27 5907.12 1.20203
301 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 11466 1.20078
Squared proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 28896.2 36767 1.27238
Rooted mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 203.673 182.638 1.11517
ALG1 Ranked beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 150.982 166.372 1.10193
302 HCK Squared tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 28896.2 36767 1.27238
PLDN Measured pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 5894.75 7073.65 1.19999
PSCD1 Rooted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 203.673 182.638 1.11517
RPL26 Ranked 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 1.10185
303 CRKL Squared crk-like protein. [swissprot;acc:p46109] 28896.2 36767 1.27238
PPP1CC Measured serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 22268.8 18560.4 1.1998
PSCD2 Rooted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 203.673 182.638 1.11517
RPL35 Ranked 60s ribosomal protein l35. [swissprot;acc:p42766] 242.333 266.999 1.10179
304 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
ABL1 Squared proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 28896.2 36767 1.27238
PRPF31 Measured pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 4855.46 5824.52 1.19958
PSCD4 Rooted cytohesin 4. [swissprot;acc:q9uia0] 203.673 182.638 1.11517
305 FYN Squared proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 28896.2 36767 1.27238
MRPL2 Ranked mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 242.339 266.986 1.1017
OSR1 Measured odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 203.673 182.638 1.11517
306 no value Measured pnas-18. [sptrembl;acc:q9bzu3] 13680.5 11409.6 1.19903
Ranked 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 1.10126
FGR Squared proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 28896.2 36767 1.27238
RBM39 Rooted rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 56.3935 62.8817 1.11505
307 CCT3 Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 14824.9 1.19892
GRAP2 Squared 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] 28896.4 36766.8 1.27237
SIN3A Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 1.11476
SRR Ranked serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 242.153 266.673 1.10126
308 AGPAT3 Squared 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] 30596.2 38919.9 1.27205
DENR Rooted density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 50.4687 45.2733 1.11476
DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 5966.44 1.19878
RPL34 Ranked 60s ribosomal protein l34. [swissprot;acc:p49207] 242.153 266.673 1.10126
309 no value Rooted u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 56.185 62.6036 1.11424
CUTL1 Squared ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 28900.8 36762.6 1.27203
DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 5966.14 1.19855
SEC61A2 Ranked protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 242.153 266.673 1.10126
310 no value Rooted myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 95.0526 85.3206 1.11406
CUTL2 Squared homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 36762.1 1.27198
SART1 Measured 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] 4909.79 5878.79 1.19736
SEC61A1 Ranked protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 266.673 1.10126
311 AGPAT4 Squared 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] 30566.4 38866.5 1.27154
DVL3 Measured segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 4981.52 5964.58 1.19734

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/