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.


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Hugo measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 2908 to 2957 of 3206 in total
Hugo
measured
Rank
description
expected
final
TFDP2 0.745698 81 TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [SWISSPROT;Acc:Q14188] 1.87445 0.397822295
TFIP11 0.398804 320 TUFTELIN-INTERACTING PROTEIN 11 (HSPC006). [SWISSPROT;Acc:Q9UBB9] 1.37218 0.290635339
TGFBR1 0.186417 1188 TGF-BETA RECEPTOR TYPE I PRECURSOR (EC 2.7.1.37) (TGFR-1) (TGF-BETA TYPE I RECEPTOR) (SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4) (SKR4) (ACTIVIN RECEPTOR-LIKE KINASE 5) (ALK-5). [SWISSPROT;Acc:P36897] 0.74967 0.248665413
TGS1 0.0391646 962 PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 0.152962 0.25604137
THBS3 0.0679913 3121 THROMBOSPONDIN 3 PRECURSOR. [SWISSPROT;Acc:P49746] 0.775204 0.087707623
THG1L 0.133213 1103 0.530672 0.251027
THNSL1 0.098396 2432 0.452567 0.217417532
THOC7 0.176498 323 0.613112 0.287872363
TIA1 0.401253 111 NUCLEOLYSIN TIA-1 (RNA-BINDING PROTEIN TIA-1) (P40-TIA-1) [CONTAINS: P15-TIA-1]. [SWISSPROT;Acc:P31483] 1.10989 0.361525016
TIAL1 0.374769 119 NUCLEOLYSIN TIAR (TIA-1 RELATED PROTEIN). [SWISSPROT;Acc:Q01085] 1.03782 0.361111753
TIMM10 0.0670247 1001 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8] 0.262934 0.254910738
TIMM22 0.0993399 393 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM22. [SWISSPROT;Acc:Q9Y584] 0.356562 0.278604843
TIMM50 0.0783783 958 0.305823 0.256286479
TIPRL 0.112123 3098 CG9578-LIKE; YEAST YPR037W AND WORM C02C2.6 PREDICTED PROTEINS-LIKE. [RefSeq;Acc:NM_152902] 1.18537 0.094589031
TKT 0.150764 2024 TRANSKETOLASE (EC 2.2.1.1) (TK). [SWISSPROT;Acc:P29401] 0.654499 0.230350237
TKTL1 0.0765571 2252 TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED PROTEIN). [SWISSPROT;Acc:P51854] 0.343091 0.223139342
TKTL2 0.130459 2057 0.567954 0.22969994
TLE2 0.304091 996 TRANSDUCIN-LIKE ENHANCER PROTEIN 2 (ESG2). [SWISSPROT;Acc:Q04725] 1.19246 0.255011489
TLE3 0.333664 984 TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [SWISSPROT;Acc:Q04726] 1.30756 0.255180642
TLE4 0.354858 974 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] 1.38936 0.255411125
TLR2 0.037683 1559 TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603] 0.156176 0.241285473
TLX1 0.0374306 873 T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314] 0.143817 0.260265476
TLX2 0.0368198 870 T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763] 0.14147 0.260265781
TLX3 0.0457909 871 T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 (HOMEOBOX PROTEIN HOX-11L2). [SWISSPROT;Acc:O43711] 0.175939 0.260265774
TM4SF19 0.048624 3089 0.498014 0.097635809
TM7SF2 0.0196287 2712 DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [SWISSPROT;Acc:O76062] 0.0946679 0.207342721
TMBIM1 0.0628846 2152 PP1201 PROTEIN. [RefSeq;Acc:NM_022152] 0.276631 0.22732304
TMBIM4 0.0343914 2154 Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24] 0.151289 0.227322542
TMCC1 0.0305282 808 0.116515 0.2620109
TMCC2 0.0377474 792 0.144067 0.262012813
TMCC3 0.0312832 798 0.119396 0.262012128
TMEM131 0.0372023 2861 RW1 PROTEIN (FRAGMENT). [SWISSPROT;Acc:Q92545] 0.196899 0.188941031
TMEM132A 0.0424223 1148 GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] 0.169541 0.250218531
TMEM132B 0.0452858 1146 0.18098 0.250225439
TMEM132C 0.0559574 1144 0.22361 0.250245517
TMEM132D 0.0465063 1145 0.185855 0.250228942
TMEM132E 0.0445191 1147 0.177917 0.250223981
TMEM189 0.298042 1610 UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 1 ISOFORM B; DNA-BINDING PROTEIN. [RefSeq;Acc:NM_003349] 1.24282 0.239811075
TMEM33 0.191364 2850 DB83 PROTEIN. [SWISSPROT;Acc:P57088] 1 0.191364
TMEM53 0.0770577 892 0.296516 0.259877039
TMEM55A 0.057982 2907 0.332958 0.174142084
TMEM64 0.0252114 2738 0.122785 0.205329641
TMEM87A 0.0425806 1045 0.168127 0.253264496
TMEM87B 0.0327294 1043 0.12923 0.253264722
TMEM91 0.0287655 2344 "2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN) (BCKDH E1-ALPHA). [SWISSPROT;Acc:P12694]" 0.130409 0.220579101
TMF1 0.0350787 2175 TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094] 0.154573 0.226939375
TMLHE 0.218407 469 "TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" 0.794482 0.274904907
TMOD1 0.0322816 2293 TROPOMODULIN 1 (ERYTHROCYTE TROPOMODULIN) (E-TMOD). [SWISSPROT;Acc:P28289] 0.145189 0.222341913
TMOD2 0.0273103 2291 NEURONAL TROPOMODULIN (N-TMOD) (TROPOMODULIN 2). [SWISSPROT;Acc:Q9NZR1] 0.12283 0.222342262
TMOD3 0.0276089 2292 UBIQUITOUS TROPOMODULIN (U-TMOD) (TROPOMODULIN 3). [SWISSPROT;Acc:Q9NYL9] 0.124173 0.222342216

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/