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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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 [...,...].
measured Hugo Rank Gene expected description final
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.0374428 SLC4A1AP 2876 0.198705 "SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]" 0.188434111
0.0374644 DEGS1 978 0.146714 SPHINGOLIPID DELTA 4 DESATURASE; MEMBRANE FATTY ACID (LIPID) DESATURASE; DIHYDROCERAMIDE DESATURASE. [RefSeq;Acc:NM_003676] 0.25535668
0.0374708 ISY1 450 0.135742 0.27604426
0.0375812 FABP4 292 0.12452 "FATTY ACID-BINDING PROTEIN, ADIPOCYTE (AFABP) (ADIPOCYTE LIPID-BINDING PROTEIN) (ALBP) (A-FABP). [SWISSPROT;Acc:P15090]" 0.301808545
0.0375954 FAM50B 1337 0.153273 DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [RefSeq;Acc:NM_012135] 0.245283905
0.0376313 LRRC4 541 0.138821 NAG14 PROTEIN. [RefSeq;Acc:NM_022143] 0.271077863
0.037683 C21orf66 1558 0.156176 GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6] 0.241285473
TLR2 1559 TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603]
0.0376832 BRF1 257 0.121057 "TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]" 0.311284767
0.0376993 FLNB 179 0.111754 "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]" 0.33734184
0.0377474 TMCC2 792 0.144067 0.262012813
0.0377549 FAP 2540 0.175918 SEPRASE (EC 3.4.21.-) (FIBROBLAST ACTIVATION PROTEIN ALPHA) (INTEGRAL MEMBRANE SERINE PROTEASE) (170-KDA MELANOMA MEMBRANE-BOUND GELATINASE). [SWISSPROT;Acc:Q12884] 0.214616469
0.037776 no value 1386 0.154523 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 0.244468461
0.0377969 SLC23A2 482 0.137792 "SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" 0.274304023
0.0378274 no value 924 0.1468 FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402] 0.257679837
0.0378287 FUT8 991 0.148317 "ALPHA-(1,6)-FUCOSYLTRANSFERASE (EC 2.4.1.68) (GLYCOPROTEIN 6-ALPHA-L- FUCOSYLTRANSFERASE) (GDP-FUCOSE--GLYCOPROTEIN FUCOSYLTRANSFERASE) (GDP-L-FUC:N-ACETYL-BETA-D-GLUCOSAMINIDE ALPHA1,6-FUCOSYLTRANSFERASE) (ALPHA1-6FUCT) (FUCOSYLTRANSFERASE 8). [SW" 0.255053028
0.0378408 SLC20A2 2363 0.171772 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]" 0.220296672
0.0378601 no value 784 0.144194 0.26256363
0.0378747 PGGT1B 926 0.146984 GERANYLGERANYL TRANSFERASE TYPE I BETA SUBUNIT (EC 2.5.1.-) (TYPE I PROTEIN GERANYL-GERANYLTRANSFERASE BETA SUBUNIT) (GGTASE-I-BETA). [SWISSPROT;Acc:P53609] 0.257679067
0.0378858 SHC3 476 0.138116 NEURONAL SHC. [RefSeq;Acc:NM_016848] 0.274304208
0.0379081 SHC2 475 0.138197 PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077] 0.274304797
0.0379775 BCAS2 519 0.139495 "BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 0.272249901
0.0379885 GATAD2A 2901 0.217449 P66 ALPHA. [RefSeq;Acc:NM_017660] 0.174700734
0.0380979 OXR1 557 0.140583 OXIDATION RESISTANCE 1. [RefSeq;Acc:NM_181354] 0.270999338
0.0381158 WDR22 1110 0.151938 0.250864168
0.0382183 RPL34 1956 0.165264 60S RIBOSOMAL PROTEIN L34. [SWISSPROT;Acc:P49207] 0.231256051
0.0382473 PRMT8 175 0.113378 PROTEIN ARGININE N-METHYLTRANSFERASE 4 (EC 2.1.1.-). [SWISSPROT;Acc:Q9NR22] 0.337343224
0.0382656 no value 2526 0.178175 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 0.214764136
0.03829 EXO1 1076 0.151786 "EXONUCLEASE 1 ISOFORM B; RAD2 NUCLEASE FAMILY MEMBER, HOMOLOG OF S. CEREVISIAE EXONUCLEASE 1. [RefSeq;Acc:NM_006027]" 0.252263055
0.038293 RPS7 1388 0.156638 40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821] 0.244468137
0.0383264 no value 2525 0.178458 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 0.214764258
0.038359 1823 0.163741 0.234266311
ANK2 1824 "ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]"
ARL3 1822 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405]
0.0383868 EXOC3 1509 0.158229 EXOCYST COMPLEX COMPONENT SEC6. [SWISSPROT;Acc:O60645] 0.24260281
0.0384193 C8orf79 418 0.138512 0.277371636
0.038432 WDR82 1392 0.157255 0.244392865
0.0384502 MAEA 1616 0.160453 0.239635283
RMND5A 1617
0.0384625 no value 1273 0.155989 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 0.246571874
SNAPAP 1274 SNARE ASSOCIATED PROTEIN SNAPIN. [RefSeq;Acc:NM_012437]
0.0385127 FAT 825 0.147402 CADHERIN-RELATED TUMOR SUPPRESSOR HOMOLOG PRECURSOR (FAT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q14517] 0.261276645
STARD3 824 MLN 64 PROTEIN (STAR-RELATED LIPID TRANSFER PROTEIN 3) (STARD3) (START DOMAIN-CONTAINING PROTEIN 3) (CAB1 PROTEIN). [SWISSPROT;Acc:Q14849]
TANC1 823
0.0385424 LATS2 553 0.142223 "LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [RefSeq;Acc:NM_014572]" 0.270999768
0.0385572 FABP7 282 0.127753 "FATTY ACID-BINDING PROTEIN, BRAIN (B-FABP) (BRAIN LIPID-BINDING PROTEIN) (BLBP) (MAMMARY DERIVED GROWTH INHIBITOR RELATED). [SWISSPROT;Acc:O15540]" 0.301810525
0.0385624 GTDC1 1119 0.153758 0.250799308
0.0385664 C16orf70 1578 0.160098 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1] 0.240892453
0.0385694 BBS7 742 0.145821 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] 0.264498255
HSDL2 743

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/