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 Rank Gene description expected final
Results: HTML CSV LaTeX Showing element 2958 to 3007 of 3206 in total
Hugo
measured
Rank
description
expected
final
TMOD4 0.0274232 2295 SKELETAL MUSCLE TROPOMODULIN (SK-TMOD) (TROPOMODULIN 4). [SWISSPROT;Acc:Q9NZQ9] 0.123338 0.222341857
TMTC4 0.0689331 1202 0.277567 0.248347606
TNFAIP1 0.281828 1142 "TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" 1.12603 0.250284628
TNFSF5IP1 0.0744175 1170 HEPATOCELLULAR CARCINOMA SUSCEPTIBILITY PROTEIN; X 003 PROTEIN; HDCMC29P; HSPC260; LIKELY ORTHOLOG OF MOUSE CD40 LIGAND-ACTIVATED SPECIFIC TRANSCRIPT 3 (CLAST3). [RefSeq;Acc:NM_020232] 0.29839 0.249396763
TNK2 0.0322816 2294 ACTIVATED P21CDC42HS KINASE. [RefSeq;Acc:NM_005781] 0.145189 0.222341913
TNPO1 0.443276 535 IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973] 1.63446 0.271206392
TNPO2 0.404881 532 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]" 1.49189 0.271387971
TNPO3 0.0647928 2247 TRANSPORTIN-SR; IMPORTIN 12. [RefSeq;Acc:NM_012470] 0.289906 0.223495892
TNS1 0.320357 779 TENSIN. [RefSeq;Acc:NM_022648] 1.21727 0.263176617
TNS3 0.283226 760 TUMOR ENDOTHELIAL MARKER 6; THYROID SPECIFIC PTB DOMAIN PROTEIN; TENSIN 3. [RefSeq;Acc:NM_022748] 1.0738 0.263760477
TOB1 0.102521 3076 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] 0.993451 0.103196836
TOB2 0.083343 3075 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] 0.807611 0.10319696
TOE1 0.12614 168 "TARGET OF EGR1, MEMBER 1 (NUCLEAR); TARGET OF EGR1, MEMBER 1. [RefSeq;Acc:NM_025077]" 0.369099 0.341751129
TOM1 0.230424 776 TARGET OF MYB PROTEIN 1. [SWISSPROT;Acc:O60784] 0.875383 0.263226496
TOM1L2 0.179057 774 TARGET OF MYB1-LIKE 2; TARGET OF MYB1 (CHICKEN) HOMOLOG-LIKE 2. [RefSeq;Acc:NM_144678] 0.680239 0.263226601
TOMM20 0.0530069 382 MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG (MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN) (OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20). [SWISSPROT;Acc:Q15388] 0.189914 0.279110018
TOMM70A 0.11844 1572 MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [SWISSPROT;Acc:O94826] 0.491473 0.240989841
TOP2B 0.249175 2554 "DNA TOPOISOMERASE II, BETA ISOZYME (EC 5.99.1.3). [SWISSPROT;Acc:Q02880]" 1.16185 0.214464001
TOP3A 0.09162 1797 DNA TOPOISOMERASE III ALPHA (EC 5.99.1.2). [SWISSPROT;Acc:Q13472] 0.390211 0.234796046
TOPBP1 0.0461407 2611 TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027] 0.218331 0.211333709
TP53BP2 0.097609 2196 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] 0.431998 0.225947805
TP53RK 0.131908 1806 P53-RELATED PROTEIN KINASE (EC 2.7.1.-) (NORI-2). [SWISSPROT;Acc:Q96S44] 0.562339 0.23457025
TPD52 0.169565 2802 TUMOR PROTEIN D52 (N8 PROTEIN). [SWISSPROT;Acc:P55327] 0.853344 0.198706501
TPD52L1 0.142496 2801 TUMOR PROTEIN D53 (HD53) (D52-LIKE 1). [SWISSPROT;Acc:Q16890] 0.71709 0.198714248
TPD52L2 0.149456 2810 TUMOR PROTEIN D54 (HD54) (D52-LIKE 2). [SWISSPROT;Acc:O43399] 0.75755 0.197288628
TPD52L3 0.0532406 2885 PROTEIN KINASE NYD-SP25. [RefSeq;Acc:NM_033516] 0.290193 0.183466176
TPI1 0.158456 2856 TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1) (TIM). [SWISSPROT;Acc:P00938] 0.830447 0.190808083
TPT1 0.06101 2147 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.268263 0.227426071
TRAPPC3 0.125021 3026 BET3 HOMOLOG. [SWISSPROT;Acc:O43617] 1.04777 0.119321034
TREH 0.0811667 2858 "TREHALASE PRECURSOR (EC 3.2.1.28) (ALPHA,ALPHA-TREHALASE) (ALPHA,ALPHA-TREHALOSE GLUCOHYDROLASE). [SWISSPROT;Acc:O43280]" 0.428605 0.189374132
TRIM2 0.285075 1632 TRIPARTITE MOTIF PROTEIN 2. [SWISSPROT;Acc:Q9C040] 1.19135 0.239287363
TRIM3 0.271838 1658 TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [SWISSPROT;Acc:O75382] 1.13816 0.238839882
TRIO 0.0734189 775 TRIPLE FUNCTIONAL DOMAIN PROTEIN (PTPRF INTERACTING PROTEIN). [SWISSPROT;Acc:O75962] 0.278919 0.2632266
TRIOBP 0.0598365 935 PROTEIN TARA (TRIO-ASSOCIATED REPEAT ON ACTIN) (HRIHFB2122). [SWISSPROT;Acc:Q9H2D6] 0.233092 0.256707652
TRIP10 0.448126 384 CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [SWISSPROT;Acc:Q15642] 1.60594 0.279042804
TRIP12 0.0325717 1767 THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [SWISSPROT;Acc:Q14669] 0.138013 0.236004579
TRIT1 0.316686 2332 TRNA ISOPENTENYLPYROPHOSPHATE TRANSFERASE. [RefSeq;Acc:NM_017646] 1.4315 0.221226685
TRMT6 0.0542439 273 0.177846 0.305004892
TRMU 0.0583389 2857 TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). [SWISSPROT;Acc:O75648] 0.30593 0.190693623
TRO 0.0662986 3133 TROPHININ. [SWISSPROT;Acc:Q12816] 1.01402 0.065381945
TRPC4 0.185352 1023 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.731277 0.253463462
TRPC5 0.2166 1026 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.854644 0.253438859
TRUB1 0.448493 1948 TRUB PSEUDOURIDINE (PSI) SYNTHASE HOMOLOG 1. [RefSeq;Acc:NM_139169] 1.93857 0.231352492
TSC22D4 0.149858 977 TSC22-RELATED INDUCIBLE LEUCINE ZIPPER PROTEIN 2 (TSC-22-LIKE PROTEIN THG-1). [SWISSPROT;Acc:Q9Y3Q8] 0.586856 0.255357362
TSEN2 0.0516003 2374 0.234495 0.220048615
TSEN34 0.0517945 2373 LENG5 PROTEIN. [RefSeq;Acc:NM_024075] 0.235377 0.220049113
TSG101 0.0655808 2937 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] 0.417367 0.157129816
TSNARE1 0.0621484 449 0.224949 0.276277734
TSNAX 0.0312503 1601 TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [SWISSPROT;Acc:Q99598] 0.130205 0.240008448
TSR1 0.263169 1831 1.12425 0.234084056

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/