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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1458 to 1507 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Value Type
red
network_comparison
green
365 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 Squared 17965.8 1.23807 22243
calcyphosine. [swissprot;acc:q13938] CAPS Measured 5189 1.17334 6088.47
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] NOL1 Rooted 49.7541 1.10428 54.9425
366 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A 50.5463 1.1042 45.7763
40s ribosomal protein s5. [swissprot;acc:p46782] RPS5 Ranked 242.473 1.09602 265.756
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] BHLHB4 Squared 62783.5 1.23628 50784.1
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] CRNKL1 Measured 5189 1.17334 6088.47
367 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] DDX18 Rooted 49.0882 1.10419 54.2027
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] BHLHB5 Squared 62757.7 1.23617 50767.8
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Measured 4024.4 1.17268 4719.35
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] HNRPM Ranked 234.146 1.09601 256.627
368 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] DRAP1 Squared 51805.2 1.23592 41916.4
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] RRP1 Rooted 49.5225 1.10418 54.6817
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 Measured 5082.66 1.17261 5959.99
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] PUS1 Ranked 242.66 1.09501 265.715
369 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] MRPL12 242.159 1.09475 265.104
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ Measured 3583.56 1.17061 4194.95
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] LGALS9 Squared 45960.8 1.23474 56749.6
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] METAP1 Rooted 49.7435 1.10397 45.0586
370 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB Measured 4108.15 1.17058 4808.93
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] METAP2 Rooted 49.7435 1.10397 45.0586
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] NUDT12 Ranked 242.159 1.09475 265.104
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] EPB41 Squared 45986 1.23464 56776.1
371 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] EPB41L1 45985.9 56776
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] RPS6KC1 Ranked 186.52 1.09447 170.42
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] HTRA2 Measured 5067.02 1.16961 5926.46
zinc finger-like protein 9. [refseq;acc:nm_033414] ZNF622 Rooted 49.3451 1.10367 54.4606
372 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] EPB41L3 Squared 45986.7 1.23464 56776.8
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] SLC45A2 Rooted 49.3451 1.10367 54.4606
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] HTRA4 Measured 5067 1.16956 5926.17
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] no value Ranked 186.52 1.09447 170.42
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] MRPL11 242.37 1.09442 265.255
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] EPB41L2 Squared 45986 1.23464 56776.1
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] no value Rooted 49.3451 1.10367 54.4606
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] HTRA3 Measured 5066.99 1.16955 5926.1
374 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 Rooted 50.2549 1.10305 45.5599
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] HTRA1 Measured 5066.93 1.16942 5925.38
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] SPTBN5 Squared 45987 1.23463 56777.1
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Ranked 267.208 1.09436 244.168
375 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] SDF4 Squared 45987 1.23463 56777.1
60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Rooted 50.2545 1.10295 45.5637
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] POLR3A Ranked 242.686 1.09407 265.516
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] LSM1 Measured 4700.42 1.16854 5492.63
376 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Rooted 50.2554 1.10285 45.5688
44050 protein. [refseq;acc:nm_178832] C10orf83 Measured 17385.9 1.16769 14889.2
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] LGALS4 Squared 46021.4 1.2345 56813.2
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 Ranked 257.017 1.09395 234.945
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] POLR1A 242.691 1.09391 265.481
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Rooted 50.2554 1.10285 45.5687
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] PPP1R8 Measured 17385.9 1.16769 14889.2

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/