[Genome] expIds

Thu Apr 3 09:07:33 PDT 2008

hello!
thanks, but i already got the table you printed for me...
my question refered to something else:
in the table hgFixed.gnfHumanAtlas2AllExps there are IDs in the range from 0 to 157 while there are just 79 expIds for human in the gnf atlas2 for expression and  regulation.
for mouse it is analog...
so is it correct to conclude that

0 ColorectalAdenocarcinoma         and 
1 ColorectalAdenocarcinoma 2
refer to the exprId 1

2,3 refer to  exprId 2
4,5 refer to exprId 3
...
156,157 refer to  exprId 78

you understand what i mean?
basically i need to get the expression-values from all common tissues in mouse and human or rather the conservation of the expression in all common tissues...
best regards!
sonja

Ann Zweig <ann at soe.ucsc.edu> wrote: Hello again Sonja,

 I have printed the contents of the tables for your use (see below).  This 
should help you correlate between mouse and human.

 In the future, please direct your questions to the genome mailing list at 
genome at soe.ucsc.edu -- our moderated forum for user questions and discussion. 
You will likely get a quicker response to your question.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

hgFixed.gnfMouseAtlas2AllExps
#id name
0 substantia nigra
1 substantia nigra 2
2 spinal cord upper
3 spinal cord upper 2
4 spinal cord lower
5 spinal cord lower 2
6 hypothalamus
7 hypothalamus 2
8 preoptic
9 preoptic 2
10 frontal cortex
11 frontal cortex 2
12 cerebral cortex
13 cerebral cortex 2
14 amygdala
15 amygdala 2
16 dorsal striatum
17 dorsal striatum 2
18 hippocampus
19 hippocampus 2
20 olfactory bulb
21 olfactory bulb 2
22 cerebellum
23 cerebellum 2
24 trigeminal
25 trigeminal 2
26 dorsal root ganglia
27 dorsal root ganglia 2
28 pituitary
29 pituitary 2
30 eye
31 eye 2
32 lymph node
33 lymph node 2
34 trachea
35 trachea 2
36 uterus
37 uterus 2
38 ovary
39 ovary 2
40 adipose tissue
41 adipose tissue 2
42 adrenal gland
43 adrenal gland 2
44 bladder
45 bladder 2
46 embryo day 10.5
47 embryo day 10.5 2
48 embryo day 9.5
49 embryo day 9.5 2
50 embryo day 8.5
51 embryo day 8.5 2
52 embryo day 7.5
53 embryo day 7.5 2
54 embryo day 6.5
55 embryo day 6.5 2
56 epidermis
57 epidermis 2
58 digits
59 digits 2
60 snout epidermis
61 snout epidermis 2
62 tongue
63 tongue 2
64 medial olfactory epithelium
65 medial olfactory epithelium 2
66 prostate
67 prostate 2
68 vomeralnasal organ
69 vomeralnasal organ 2
70 lung
71 lung 2
72 umbilical cord
73 umbilical cord 2
74 stomach
75 stomach 2
76 large intestine
77 large intestine 2
78 bone marrow
79 bone marrow 2
80 bone
81 bone 2
82 spleen
83 spleen 2
84 thymus
85 thymus 2
86 B220+ B-cells
87 B220+ B-cells 2
88 CD4+T-cells
89 CD4+T-cells 2
90 CD8+T-cells
91 CD8+T-cells 2
92 brown fat
93 brown fat 2
94 heart
95 heart 2
96 skeletal muscle
97 skeletal muscle 2
98 placenta
99 placenta 2
100 mammary gland (lact)
101 mammary gland (lact) 2
102 blastocysts
103 blastocysts 2
104 kidney
105 kidney 2
106 small intestine
107 small intestine 2
108 salivary gland
109 salivary gland 2
110 thyroid
111 thyroid 2
112 liver
113 liver 2
114 fertilized egg
115 fertilized egg 2
116 oocyte
117 oocyte 2
118 pancreas
119 pancreas 2
120 testis
121 testis 2

hgFixed.gnfHumanAtlas2AllExps
#id name
0 ColorectalAdenocarcinoma
1 ColorectalAdenocarcinoma 2
2 WHOLEBLOOD
3 WHOLEBLOOD 2
4 BM-CD33+Myeloid
5 BM-CD33+Myeloid 2
6 PB-CD14+Monocytes
7 PB-CD14+Monocytes 2
8 PB-BDCA4+Dentritic Cells
9 PB-BDCA4+Dentritic Cells 2
10 PB-CD56+NKCells
11 PB-CD56+NKCells 2
12 PB-CD4+Tcells
13 PB-CD4+Tcells 2
14 PB-CD8+Tcells
15 PB-CD8+Tcells 2
16 PB-CD19+Bcells
17 PB-CD19+Bcells 2
18 BM-CD105+Endothelial
19 BM-CD105+Endothelial 2
20 BM-CD34+
21 BM-CD34+ 2
22 leukemialymphoblastic(molt4)
23 leukemialymphoblastic(molt4) 2
24 721 B lymphoblasts
25 721 B lymphoblasts 2
26 lymphomaburkittsRaji
27 lymphomaburkittsRaji 2
28 leukemiapromyelocytic(hl60)
29 leukemiapromyelocytic(hl60) 2
30 lymphomaburkittsDaudi
31 lymphomaburkittsDaudi 2
32 leukemiachronicmyelogenous(k562)
33 leukemiachronicmyelogenous(k562) 2
34 thymus
35 thymus 2
36 Tonsil
37 Tonsil 2
38 lymphnode
39 lymphnode 2
40 fetalliver
41 fetalliver 2
42 BM-CD71+EarlyErythroid
43 BM-CD71+EarlyErythroid 2
44 bonemarrow
45 bonemarrow 2
46 TemporalLobe
47 TemporalLobe 2
48 globuspallidus
49 globuspallidus 2
50 CerebellumPeduncles
51 CerebellumPeduncles 2
52 cerebellum
53 cerebellum 2
54 caudatenucleus
55 caudatenucleus 2
56 WholeBrain
57 WholeBrain 2
58 ParietalLobe
59 ParietalLobe 2
60 MedullaOblongata
61 MedullaOblongata 2
62 Amygdala
63 Amygdala 2
64 PrefrontalCortex
65 PrefrontalCortex 2
66 OccipitalLobe
67 OccipitalLobe 2
68 Hypothalamus
69 Hypothalamus 2
70 Thalamus
71 Thalamus 2
72 subthalamicnucleus
73 subthalamicnucleus 2
74 CingulateCortex
75 CingulateCortex 2
76 Pons
77 Pons 2
78 spinalcord
79 spinalcord 2
80 fetalbrain
81 fetalbrain 2
82 adrenalgland
83 adrenalgland 2
84 Lung
85 Lung 2
86 Heart
87 Heart 2
88 Liver
89 Liver 2
90 kidney
91 kidney 2
92 Prostate
93 Prostate 2
94 Uterus
95 Uterus 2
96 Thyroid
97 Thyroid 2
98 fetalThyroid
99 fetalThyroid 2
100 fetallung
101 fetallung 2
102 PLACENTA
103 PLACENTA 2
104 CardiacMyocytes
105 CardiacMyocytes 2
106 SmoothMuscle
107 SmoothMuscle 2
108 bronchialepithelialcells
109 bronchialepithelialcells 2
110 ADIPOCYTE
111 ADIPOCYTE 2
112 Pancreas
113 Pancreas 2
114 PancreaticIslets
115 PancreaticIslets 2
116 testis
117 testis 2
118 TestisLeydigCell
119 TestisLeydigCell 2
120 TestisGermCell
121 TestisGermCell 2
122 TestisInterstitial
123 TestisInterstitial 2
124 TestisSeminiferousTubule
125 TestisSeminiferousTubule 2
126 salivarygland
127 salivarygland 2
128 trachea
129 trachea 2
130 AdrenalCortex
131 AdrenalCortex 2
132 Ovary
133 Ovary 2
134 Appendix
135 Appendix 2
136 skin
137 skin 2
138 ciliaryganglion
139 ciliaryganglion 2
140 TrigeminalGanglion
141 TrigeminalGanglion 2
142 atrioventricularnode
143 atrioventricularnode 2
144 DRG
145 DRG 2
146 SuperiorCervicalGanglion
147 SuperiorCervicalGanglion 2
148 SkeletalMuscle
149 SkeletalMuscle 2
150 UterusCorpus
151 UterusCorpus 2
152 TONGUE
153 TONGUE 2
154 OlfactoryBulb
155 OlfactoryBulb 2
156 Pituitary
157 Pituitary 2

sonja althammer wrote:
> hello ann!
> thanks a lot! i found the tables i was looking for!
> but what i still do not understand about the tables is, why #id (in 
> hgFixed.gnfHumanAtlas2AllExps) is in the range from 0 to 157 while there 
> are just 79 expIds for human in the gnf atlas2 for expression and 
> regulation.
> for mouse it is analog...
> as the tissues appear twice, do i conclude right like this:
> to get the according tissue to expId 79 i select #id 156 from 
> hgFixed.gnfHumanAtlas2AllExps (expId*2 -2)
> 
> in the end i want to work with the intersection of the tissues in human 
> and mouse...
> best regards!
> sonja
> 
> */Ann Zweig /* wrote:
> 
>     Hello Sonja,
> 
>     You can find the tissue types for each of the GNF Atlas 2 tracks in the
>     corresponding tables in the hgFixed database:
> 
>     gnfHumanAtlas2AllExps
>     gnfMouseAtlas2AllExps
> 
>     To explore the contents of database tables, use the Table Browser tool
>     on the website ('Tables' from the top blue navigation bar).
> 
>     group: All Tables
>     database: hgFixed
>     table: hgFixed.gnfHumanAtlas2AllExps
> 
>     output format: all fields from selected table
> 
>     The id and name fields contain the information you are looking for.
>     For example, from the hgFixed.gnfHumanAtlas2AllExps table, the first 5
>     rows are:
> 
>     #id name
>     0 ColorectalAdenocarcinoma
>     1 ColorectalAdenocarcinoma 2
>     2 WHOLEBLOOD
>     3 WHOLEBLOOD 2
>     4 BM-CD33+Myeloid
> 
> 
>     You might also be interested in reading the paper associated with this
>     track: http://www.pnas.org/cgi/content/abstract/101/16/6062
> 
>     I hope this information is helpful to you. Please don't hesitate to
>     contact the mail list again if you require further assistance.
> 
>     Regards,
> 
>     ----------
>     Ann Zweig
>     UCSC Genome Bioinformatics Group
>     http://genome.ucsc.edu
> 
>     Please feel free to search the Genome mailing list archives by visiting
>     our home page, clicking on "Contact Us", then typing a word or phrase
>     into the search box. On that same page
>     (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome
>     mailing list.
> 
> 
> 
> 
> 
> 
>     sonja althammer wrote:
>      > browsing the expression data from the gnf atlas2 my question arose:
>      > are the expression-Ids equal for human and mouse, i.e. do they
>     refer to the same type of tissue?
>      > best regards!
>      >
>      >
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