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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2901 to 2950 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Value Type
Interaction Map
red
green
network_comparison
363 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Measured Low confidence 9099.15 9593.54 1.05433
PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 71.4038 74.9877 1.05019
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked High confidence 231.481 211.131 1.09639
TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared 57579.2 46497.2 1.23834
364 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted 50.0785 55.3215 1.1047
DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked Low confidence 212.235 204.495 1.03785
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured High confidence 5189 6088.47 1.17334
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Low confidence 7711.11 8129.27 1.05423
MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Squared 47813.3 44628.6 1.07136
POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked High confidence 243.208 266.617 1.09625
SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared 17957.2 22234.1 1.23817
SYNJ1 synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Rooted Low confidence 72.885 76.5357 1.05009
365 no value pnas-129. [sptrembl;acc:q9bxv8] Squared 47804.5 44622.6 1.07131
BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 17965.8 22243 1.23807
CAPS calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 242.744 266.07 1.09609
NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 49.7541 54.9425 1.10428
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 71.3292 74.8889 1.04991
SLC26A9 solute carrier family 26, member 9 isoform b; anion transporter/exchanger-9. [refseq;acc:nm_134325] Measured 8452.93 8910.99 1.05419
SPAG7 sperm associated antigen 7. [refseq;acc:nm_004890] Ranked 117.525 121.959 1.03773
366 BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared High confidence 62783.5 50784.1 1.23628
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 5189 6088.47 1.17334
MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Squared Low confidence 47796.9 44617.4 1.07126
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 70.5037 74.0176 1.04984
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 50.5463 45.7763 1.1042
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
SLC26A5 prestin. [swissprot;acc:p58743] Measured Low confidence 8452.93 8910.99 1.05419
ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Ranked 207.433 199.944 1.03746
367 no value 60s ribosomal protein l21. [swissprot;acc:p46778] Measured 8452.93 8910.99 1.05419
BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared High confidence 62757.7 50767.8 1.23617
DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted 49.0882 54.2027 1.10419
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 1.09601
POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured 4024.4 4719.35 1.17268
SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Ranked Low confidence 206.945 199.503 1.0373
SYNJ2 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Rooted 72.8686 76.496 1.04978
ZNF547 sedlin. [swissprot;acc:o14582] Squared 56121.2 60110.1 1.07108
368 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured High confidence 5082.66 5959.99 1.17261
DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 51805.2 41916.4 1.23592
OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Rooted Low confidence 85.1252 89.3577 1.04972
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked High confidence 242.66 265.715 1.09501
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 1.10418
RTN4IP1 reticulon 4 interacting protein 1; nogo-interacting mitochondrial protein. [refseq;acc:nm_032730] Squared Low confidence 49403.7 46150.8 1.07048
SLC26A4 pendrin (sodium-independent chloride/iodide transporter). [swissprot;acc:o43511] Measured 8452.93 8910.99 1.05419
SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Ranked 219.655 211.763 1.03727
369 no value solute carrier family 26 member 6 (pendrin-like protein 1) (pendrin l1). [swissprot;acc:q9bxs9] Measured 8452.93 8910.99 1.05419
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] High confidence 3583.56 4194.95 1.17061
KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Squared Low confidence 53052.9 49563.7 1.0704
LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] High confidence 45960.8 56749.6 1.23474
METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Ranked 242.159 265.104 1.09475

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/